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  • Molecular Diversity Preservation International (MDPI)
  • American Geophysical Union (AGU)
  • Annual Reviews
  • 2015-2019  (1.249)
  • 1980-1984
  • 1935-1939
  • 2017  (1.249)
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  • 2015-2019  (1.249)
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  • 1
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Annual Review of Marine Science 9 (2017): 173-203, doi:10.1146/annurev-marine-010816-060733.
    Beschreibung: The events that followed the Tohoku earthquake and tsunami on March 11, 2011, included the loss of power and overheating at the Fukushima Daiichi nuclear power plants, which led to extensive releases of radioactive gases, volatiles, and liquids, particularly to the coastal ocean. The fate of these radionuclides depends in large part on their oceanic geochemistry, physical processes, and biological uptake. Whereas radioactivity on land can be resampled and its distribution mapped, releases to the marine environment are harder to characterize owing to variability in ocean currents and the general challenges of sampling at sea. Five years later, it is appropriate to review what happened in terms of the sources, transport, and fate of these radionuclides in the ocean. In addition to the oceanic behavior of these contaminants, this review considers the potential health effects and societal impacts.
    Beschreibung: K.B. was supported in part by the Gordon and Betty Moore Foundation and the Deerbrook Charitable Trust. P.M. was supported in part by the Generalitat de Catalunya through MERS (grant 2014 SGR 1356), the European Commission 7th Framework COMET-FRAME project (grant agreement 604974), and the Ministerio de Economía y Competitividad of Spain (project CTM2011-15152-E). S.C. was supported in part by the French program Investissement d'Avenir run by the National Research Agency (AMORAD project, grant ANR-11-RSNR-0002). D.O. was supported in part by the Center for Environmental Radioactivity (NFR Centers of Excellence grant 223268/F50). J.N.S. was supported in part by the Marine Environmental Observation, Prediction, and Response Network.
    Schlagwort(e): Cesium ; Caesium ; North Pacific ; Radioactivity ; Japan
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
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  • 2
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    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publikationsdatum: 2017-02-10
    Beschreibung: Cellular stress‐induced temporal alterations—i.e., dynamics—are typically exemplified  by the dynamics of p53 that serve as a master to determine cell fate. p53 dynamics were initially  identified as the variations of p53 protein levels. However, a growing number of studies have  shown that p53 dynamics are also manifested in variations in the activity, spatial location, and  posttranslational modifications of p53 proteins, as well as the interplay among all p53 dynamical  features. These are essential in determining a specific outcome of cell fate. In this review, we  discuss the importance of the multifaceted features of p53 dynamics and their roles in the cell fate  decision process, as well as their potential applications in p53‐based cancer therapy. The review  provides new insights into p53 signaling pathways and their potentials in the development of new  strategies in p53‐based cancer therapy.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 3
    Publikationsdatum: 2017-01-01
    Beschreibung: The historical developments are reviewed that have led from a bottom-up responsibility initiative of concerned scientists to the emergence of a nationwide interdisciplinary Priority Program on the assessment of Climate Engineering (CE), funded by the German Research Foundation (DFG). Given the perceived lack of comprehensive and comparative appraisals of different CE methods, the Priority Program was designed to encompass both solar radiation management (SRM) and carbon dioxide removal (CDR) ideas, and to cover the atmospheric, terrestrial and oceanic realm. First key findings obtained by the ongoing Priority Program are summarized and reveal that compared to earlier assessments, such as the 2009 Royal Society report, more detailed investigations tend to indicate less efficiency, lower effectiveness and often lower safety. Emerging research trends are discussed in the context of the recent Paris agreement to limit global warming to less than two degrees and the associated increasing reliance on negative emission technologies. Our results show then when deployed at scales large enough to have a significant impact on atmospheric CO 2 , even CDR methods such as afforestation – often perceived as ‘benign’ – can have substantial side effects and may raise severe ethical, legal and governance issues. We suppose that before being deployed at climatically relevant scales, any negative-emission or climate engineering method will require careful analysis of efficiency, effectiveness and undesired side effects.
    Digitale ISSN: 2328-4277
    Thema: Geologie und Paläontologie
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  • 4
    Publikationsdatum: 2017-01-01
    Beschreibung: Since 1960's, India experiences a series of extreme drought and flood events during the summer months. The Humid Subtropical Climatic Zone (HSTC), which comprises the Indo-Gangetic Plain (IGP) region of India, is highly vulnerable to the climatic extremities. This region is the home for ~40% of total population and yields ~50% of total agricultural production of India. We investigate the historical variation in dry/wet conditions and project the future changes in extreme events under two different scenarios of the CMIP5 models. Firstly, the model parameters i.e. precipitation ( P ) and temperature ( T ) are bias corrected with respect to observation data and finally 6 models are selected, which are in right phase with the observation for composite analysis. Next, we calculate the potential evapo-transpiration ( PET ) and the Standardized Potential Evapo-transpiration Index ( SPEI ) to characterize the extreme events. Both P and PET are projected to increase in the HSTC zone; however, both the wet and dry conditions demonstrate a persistent increase in future. In relative terms, P increases faster than PET along the Gangetic Plain region (wet condition) and decreases in the southern and eastern part of the region (dry condition). The mitigating effect (RCP4.5 scenario) of precipitation increase will be overridden by strengthened PET and extreme dry condition project markedly under RCP8.5 scenario. The features are consistent with the increase/ decrease in multi-model mean SPEI, consistent with the spatial pattern of P−PET . The area affected due to wet and dry events will be relatively higher under the RCP4.5 and RCP8.5 scenario, respectively.
    Digitale ISSN: 2328-4277
    Thema: Geologie und Paläontologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 5
    Publikationsdatum: 2017-08-19
    Beschreibung: Genes, Vol. 8, Pages 203: Transcriptome Analysis Reveals Long Intergenic Noncoding RNAs Contributed to Growth and Meat Quality Differences between Yorkshire and Wannanhua Pig Genes doi: 10.3390/genes8080203 Authors: Cheng Zou Sha Li Lulu Deng Yang Guan Dake Chen Xiongkun Yuan Tianrui Xia Xinglin He Yawei Shan Changchun Li There are major differences between Yorkshire (lean-type) and Wannanhua pig (fat-type) in terms of growth performance and meat quality. Long intergenic noncoding RNAs (lincRNAs) are a class of regulators that are involved in numerous biological processes and widely identified in many species. However, the role of lincRNAs in pig is largely unknown, and the mechanisms by which they affect growth and meat quality are elusive. In this study, we used published data to identify 759 lincRNAs in porcine longissimus dorsi muscle. These putative lincRNAs shared many features with mammalian lincRNAs, such as shorter length and fewer exons. Gene ontology and pathway analysis indicated that many potential target genes (PTGs) of lincRNAs were involved in muscle growth-related and meat quality-related biological processes. Moreover, we constructed a co-expression network between differentially expressed lincRNAs (DELs) and their PTGs, and found a potential mechanism that most DELs can use to upregulate their PTGs, which may finally contribute to the growth and meat quality differences between the two breeds through an unknown manner. This work details some lincRNAs and their PTGs related to muscle growth or meat quality, and facilitates future research on the roles of lincRNAs in these two types of pig, as well as molecular-assisted breeding for pig.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 6
    Publikationsdatum: 2017-08-26
    Beschreibung: Genes, Vol. 8, Pages 202: Auxin Response Factor Genes Repertoire in Mulberry: Identification, and Structural, Functional and Evolutionary Analyses Genes doi: 10.3390/genes8090202 Authors: Vinay Baranwal Nisha Negi Paramjit Khurana Auxin Response Factors (ARFs) are at the core of the regulation mechanism for auxin-mediated responses, along with AUX/IAA proteins.They are critical in the auxin-mediated control of various biological responses including development and stress. A wild mulberry species genome has been sequenced and offers an opportunity to investigate this important gene family. A total of 17 ARFs have been identified from mulberry (Morus notabilis) which show a wide range of expression patterns. Of these 17 ARFs, 15 have strong acidic isoelectric point (pI) values and a molecular mass ranging from 52 kDa to 101 kDa. The putative promoters of these ARFs harbour cis motifs related to light-dependent responses, various stress responses and hormone regulations suggestive of their multifactorial regulation. The gene ontology terms for ARFs indicate their role in flower development, stress, root morphology and other such development and stress mitigation related activities. Conserved motif analysis showed the presence of all typical domains in all but four members that lack the PB1 domain and thus represent truncated ARFs. Expression analysis of these ARFs suggests their preferential expression in tissues ranging from leaf, root, winter bud, bark and male flowers. These ARFs showed differential expression in the leaf tissue of M. notabilis, Morus laevigata and Morus serrata. Insights gained from this analysis have implications in mulberry improvement programs.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 7
    Publikationsdatum: 2017-08-25
    Beschreibung: Genes, Vol. 8, Pages 210: Whole Genome Sequencing Revealed Mutations in Two Independent Genes as the Underlying Cause of Retinal Degeneration in an Ashkenazi Jewish Pedigree Genes doi: 10.3390/genes8090210 Authors: Kevin Gustafson Jacque Duncan Pooja Biswas Angel Soto-Hermida Hiroko Matsui David Jakubosky John Suk Amalio Telenti Kelly Frazer Radha Ayyagari Retinitis pigmentosa (RP) causes progressive photoreceptor loss resulting from mutations in over 80 genes. This study identified the genetic cause of RP in three members of a non-consanguineous pedigree. Detailed ophthalmic evaluation was performed in the three affected family members. Whole exome sequencing (WES) and whole genome sequencing (WGS) were performed in the three affected and the two unaffected family members and variants were filtered to detect rare, potentially deleterious variants segregating with disease. WES and WGS did not identify potentially pathogenic variants shared by all three affected members. However, WES identified a previously reported homozygous nonsense mutation in KIZ (c.226C>T, p.Arg76*) in two affected sisters, but not in their affected second cousin. WGS revealed a novel 1.135 kb homozygous deletion in a retina transcript of C21orf2 and a novel 30.651 kb heterozygous deletion in CACNA2D4 in the affected second cousin. The sisters with the KIZ mutation carried no copies of the C21orf2 or CACNA2D4 deletions, while the second cousin with the C21orf2 and CACNA2D4 deletions carried no copies of the KIZ mutation. This study identified two independent, homozygous mutations in genes previously reported in autosomal recessive RP in a non-consanguineous family, and demonstrated the value of WGS when WES fails to identify likely disease-causing mutations.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 8
    Publikationsdatum: 2017-09-01
    Beschreibung: Genes, Vol. 8, Pages 216: X Chromosome Evolution in Cetartiodactyla Genes doi: 10.3390/genes8090216 Authors: Anastasia Proskuryakova Anastasia Kulemzina Polina Perelman Alexey Makunin Denis Larkin Marta Farré Anna Kukekova Jennifer Lynn Johnson Natalya Lemskaya Violetta Beklemisheva Melody Roelke-Parker June Bellizzi Oliver Ryder Stephen O’Brien Alexander Graphodatsky The phenomenon of a remarkable conservation of the X chromosome in eutherian mammals has been first described by Susumu Ohno in 1964. A notable exception is the cetartiodactyl X chromosome, which varies widely in morphology and G-banding pattern between species. It is hypothesized that this sex chromosome has undergone multiple rearrangements that changed the centromere position and the order of syntenic segments over the last 80 million years of Cetartiodactyla speciation. To investigate its evolution we have selected 26 evolutionarily conserved bacterial artificial chromosome (BAC) clones from the cattle CHORI-240 library evenly distributed along the cattle X chromosome. High-resolution BAC maps of the X chromosome on a representative range of cetartiodactyl species from different branches: pig (Suidae), alpaca (Camelidae), gray whale (Cetacea), hippopotamus (Hippopotamidae), Java mouse-deer (Tragulidae), pronghorn (Antilocapridae), Siberian musk deer (Moschidae), and giraffe (Giraffidae) were obtained by fluorescent in situ hybridization. To trace the X chromosome evolution during fast radiation in specious families, we performed mapping in several cervids (moose, Siberian roe deer, fallow deer, and Pere David’s deer) and bovid (muskox, goat, sheep, sable antelope, and cattle) species. We have identified three major conserved synteny blocks and rearrangements in different cetartiodactyl lineages and found that the recently described phenomenon of the evolutionary new centromere emergence has taken place in the X chromosome evolution of Cetartiodactyla at least five times. We propose the structure of the putative ancestral cetartiodactyl X chromosome by reconstructing the order of syntenic segments and centromere position for key groups.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 9
    Publikationsdatum: 2017-09-02
    Beschreibung: Genes, Vol. 8, Pages 218: 3D Microstructure Inhibits Mesenchymal Stem Cells Homing to the Site of Liver Cancer Cells on a Microchip Genes doi: 10.3390/genes8090218 Authors: Xingyuan Yang Xinyue Xu Yuan Zhang Weijia Wen Xinghua Gao The cell microenvironment consists of multiple types of biophysical and biochemical factors, and represents a complex integrated system that is variable in both time and space. Studies show that changes in biochemical and biophysical factors in cell microenvironments result in significant changes in cellular forms and functions, especially for stem cells. Mesenchymal stem cells (MSCs) are derived from adult stem cells of the mesoderm and play an important role in tissue engineering, regenerative medicine and even cancer therapy. Furthermore, it is found that MSCs can interact with multiple types of tumor cells. The interaction is reflected as two totally different aspects. The negative aspect is that MSCs manifest as tumor-associated fibroblasts and could induce migration of cancer cells and promote tumor formation. On the other hand, MSCs can home to sites of the tumor microenvironment, directionally migrate toward tumor cells and cause tumor cell apoptosis. In this study, we designed and made a simple microfluidic chip for cell co-culture, and studied stem cell homing behavior in the interaction between MSCs and liver cancer cells. Moreover, by etching a three-dimensional microstructure on the base and adding transforming growth factor-β (TGF-β) in the co-culture environment, we studied the impact of biophysical and biochemical factors on stem cell homing behavior, and the causes of such impact.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 10
    Publikationsdatum: 2017-09-06
    Beschreibung: In the 2000s, the rapid growth of CO 2 emitted in the production of exports from developing to developed countries, in which China accounted for the dominant share, led to concerns that climate polices had been undermined by international trade. Arguments on ‘carbon leakage’ and ‘competitiveness’ – which led to the refusal of the United States to ratify the Kyoto Protocol – put pressure on developing countries, especially China, to limit their emissions with Border Carbon Adjustments used as one threat. After strong growth in the early 2000s, emissions exported from developing to developed countries plateaued and could have even decreased since 2007. These changes were mainly due to China: In 2002–2007, China’s exported emissions grew by 827 MtCO 2 , amounting to almost all the 892 MtCO 2 total increase in emissions exported from developing to developed countries, while in 2007–2012, emissions exported from China decreased by 229 MtCO 2 , contributing to the total decrease of 172 MtCO 2 exported from developing to developed countries. We apply Structural Decomposition Analysis to find that, in addition to the diminishing effects of the global financial crisis, the slowdown and eventual plateau was largely explained by several potentially permanent changes in China: Decline in export volume growth, improvements in CO 2 intensity, and changes in production structure and the mix of exported products. We argue that growth in China’s exported emissions will not return to the high levels during the 2000s, therefore the arguments for climate polices focused on embodied emissions such as Border Carbon Adjustments are now weakened.
    Digitale ISSN: 2328-4277
    Thema: Geologie und Paläontologie
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  • 11
    Publikationsdatum: 2017-08-19
    Beschreibung: Genes, Vol. 8, Pages 204: Variation in the Ovine KAP6-3 Gene (KRTAP6-3) Is Associated with Variation in Mean Fibre Diameter-Associated Wool Traits Genes doi: 10.3390/genes8080204 Authors: Shaobin Li Huitong Zhou Hua Gong Fangfang Zhao Jiqing Wang Yuzhu Luo Jon Hickford Polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) analysis was used to investigate variation in the ovine KAP6-3 gene (KRTAP6-3) in 383 Merino × Southdown-cross lambs from four sire-lines, and to determine whether this variation affects wool traits. Five PCR-SSCP banding patterns, representing five different nucleotide sequences, were detected, including four previously identified (named A, B, C, and F) variants and one newly identified (named G) variant. A new non-synonymous single nucleotide polymorphism (SNP) and a 45-bp deletion were detected in variant G. Of the three common genotypes (AA, AB, and AG) identified in these sheep, wool from sheep that were AG, on average, had a lower mean fibre diameter (MFD), fibre diameter standard deviation (FDSD), and prickle factor (PF) than wool from AA sheep, whereas wool from AB sheep, on average, had a higher MFD, FDSD, and PF than wool from AA sheep. This suggests that variation in ovine KRTAP6-3 affect MFD, FDSD, and PF, and that this gene may have potential for use as a gene-maker for improving fibre diameter-associated wool traits.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 12
    Publikationsdatum: 2017-08-19
    Beschreibung: Genes, Vol. 8, Pages 205: Mapping of QTLs for Seed Phorbol Esters, a Toxic Chemical in Jatropha curcas (L.) Genes doi: 10.3390/genes8080205 Authors: Kitiya Amkul Kularb Laosatit Prakit Somta Sangrea Shim Suk-Ha Lee Patcharin Tanya Peerasak Srinives Jatropha (Jatropha curcas L.) is an oil-bearing plant that has potential to be cultivated as a biodiesel crop. The seed cake after oil extraction has 40–50% protein that can be used in animal feeds. A major limitation in utilizing the cake is the presence of phorbol esters (PE), a heat-tolerant toxic chemical. To identify the quantitative trait loci (QTLs) for PE, we constructed a genetic linkage map from an F2 population of 95 individuals from a cross “Chai Nat” × “M10” using 143 simple sequence repeat (SSR) markers. M10 is low in seed PE while Chai Nat is high. Seeds from each F2 individual were quantified for PE content by high performance liquid chromatography. A single marker analysis revealed five markers from linkage group 3 (LG3) and nine markers from LG8 associated with seed PE. Inclusive composite interval mapping identified two QTLs, each on LG3 (qPE3.1) and LG8 (qPE8.1) responsible for the PE. qPE3.1 and qPE8.1 accounted for 14.10%, and 15.49% of total variation in seed PE, respectively. Alelle(s) from M10 at qPE3.1 increased seed PE, while at qPE8.1 decreased seed PE. qPE3.1 is a new loci for PE, while qPE8.1 is the same locus with that reported recently for PE.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 13
    Publikationsdatum: 2017-08-22
    Beschreibung: Genes, Vol. 8, Pages 206: Viral Infection Identifies Micropeptides Differentially Regulated in smORF-Containing lncRNAs Genes doi: 10.3390/genes8080206 Authors: Brandon Razooky Benedikt Obermayer Joshua O’May Alexander Tarakhovsky Viral infection leads to a robust cellular response whereby the infected cell produces hundreds of molecular regulators to combat infection. Currently, non-canonical components, e.g., long noncoding RNAs (lncRNAs) have been added to the repertoire of immune regulators involved in the antiviral program. Interestingly, studies utilizing next-generation sequencing technologies show that a subset of the >10,000 lncRNAs in the mammalian genome contain small open reading frames (smORFs) associated with active translation, i.e., many lncRNAs are not noncoding. Here, we use genome-wide high-throughput methods to identify potential micropeptides in smORF-containing lncRNAs involved in the immune response. Using influenza as a viral infection model, we performed RNA-seq and ribosome profiling to track expression and translation of putative lncRNAs that may encode for peptides and identify tens of potential candidates. Interestingly, many of these peptides are highly conserved at the protein level, strongly suggesting biological relevance and activity. By perusing publicly available data sets, four potential peptides of interest seem common to stress induction and/or are highly conserved; potential peptides from the MMP24-AS1, ZFAS1, RP11-622K12.1, and MIR22HG genes. Interestingly, using an antibody against the potential peptide encoded by MIR22HG RNA, we show that the peptide is stably expressed in the absence of infection, and upregulated in response to infection, corroborating the prediction of the ribosome profiling results. These data show the utility of perturbation approaches in identifying potentially relevant novel molecules encoded in the genome.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 14
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    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publikationsdatum: 2017-08-23
    Beschreibung: Genes, Vol. 8, Pages 209: The Genetic Architecture of Type 1 Diabetes Genes doi: 10.3390/genes8080209 Authors: Samuel Jerram Richard David Leslie Type 1 diabetes (T1D) is classically characterised by the clinical need for insulin, the presence of disease-associated serum autoantibodies, and an onset in childhood. The disease, as with other autoimmune diseases, is due to the interaction of genetic and non-genetic effects, which induce a destructive process damaging insulin-secreting cells. In this review, we focus on the nature of this interaction, and how our understanding of that gene–environment interaction has changed our understanding of the nature of the disease. We discuss the early onset of the disease, the development of distinct immunogenotypes, and the declining heritability with increasing age at diagnosis. Whilst Human Leukocyte Antigens (HLA) have a major role in causing T1D, we note that some of these HLA genes have a protective role, especially in children, whilst other non-HLA genes are also important. In adult-onset T1D, the disease is often not insulin-dependent at diagnosis, and has a dissimilar immunogenotype with reduced genetic predisposition. Finally, we discuss the putative nature of the non-genetic factors and how they might interact with genetic susceptibility, including preliminary studies of the epigenome associated with T1D.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 15
    Publikationsdatum: 2017-08-23
    Beschreibung: Genes, Vol. 8, Pages 207: Long Noncoding RNAs as Diagnostic and Therapeutic Targets in Type 2 Diabetes and Related Complications Genes doi: 10.3390/genes8080207 Authors: Fatjon Leti Johanna DiStefano Protein-coding genes represent only a small fraction of the human genome. In the past, the majority of the genomic sequence has been considered transcriptionally silent, but recent large-scale studies have uncovered an array of functionally significant elements, including non-protein-coding transcripts, within these noncoding regions of the human genome. Long noncoding RNAs (lncRNAs), a class of noncoding transcripts with lengths >200 nucleotides, are pervasively transcribed in the genome and function as signals, decoys, guides, or scaffolds to regulate gene expression. More than 200 diseases have been associated with dysregulated or dysfunctional lncRNAs, and new associations continue to accumulate in the literature. The role of lncRNAs in the pathogenesis of type 2 diabetes mellitus and related complications has only recently been recognized, but there is already evidence for their involvement in many of the pathophysiological mechanisms underlying the disease. In this review, we summarize the current knowledge of the functions and underlying mechanisms of lncRNA activity with a focus on type 2 diabetes mellitus and related renal and retinal complications of the disease. We also discuss the potential of lncRNAs to serve as therapeutic targets for drug development and diagnostic markers for clinical applications in the management of diabetes.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 16
    Publikationsdatum: 2017-09-02
    Beschreibung: We present new detail on how future SLR will modify nonlinear wave transformation processes, shoreline wave energy and wave driven flooding on atoll islands. Frequent and destructive wave inundation is a primary climate-change hazard that may render atoll islands uninhabitable in the near future. However, limited research has examined the physical vulnerability of atoll islands to future SLR and sparse information is available to implement process based coastal management on coral reef environments. We utilize a field-verified numerical model capable of resolving all nonlinear wave transformation processes to simulate how future SLR will modify wave dissipation and overtopping on Funafuti Atoll, Tuvalu, accounting for static and accretionary reef adjustment morphologies. Results show that future SLR coupled with a static reef morphology will not only increase shoreline wave energy and overtopping but will fundamental alter the spectral composition of shoreline energy by decreasing the contemporary influence of low frequency infragravity waves. ‘ Business-as-usual ' emissions (RCP 8.5) will result in annual wave overtopping on Funafuti Atoll by 2030, with overtopping at high tide under mean wave conditions occurring from 2090. Comparatively, vertical reef accretion in response to SLR will prevent any significant increase in shoreline wave energy and mitigate wave driven flooding volume by 72%. Our results provide the first quantitative assessment of how effective future reef accretion can be at mitigating SLR associated flooding on atoll islands and endorse active reef conservation and restoration for future coastal protection.
    Digitale ISSN: 2328-4277
    Thema: Geologie und Paläontologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 17
    Publikationsdatum: 2017-09-06
    Beschreibung: ABSTRACT Risk perception research has played an influential role in supporting risk management and risk communication policy. Risk perception studies are popular across a range of disciplines in the social and natural sciences for a wide range of hazard types. Their results have helped to articulate the complex individual, relational, structural, and environmental factors influencing people's behavior. Connections between individual and collective behaviors and norms impacting global climate change, and consequently, local disaster risk, however, are infrequently included in disaster risk management. This paper presents results from two diverse and complementary European risk perception studies examining both natural and anthropogenic hazards. Research gaps and recommendations for developing more comprehensive risk management strategies are presented.
    Digitale ISSN: 2328-4277
    Thema: Geologie und Paläontologie
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  • 18
    Publikationsdatum: 2017-09-06
    Beschreibung: Genes, Vol. 8, Pages 219: Quantification of Pseudouridine Levels in Cellular RNA Pools with a Modified HPLC-UV Assay Genes doi: 10.3390/genes8090219 Authors: Jialin Xu Alice Gu Naresh Thumati Judy Wong Pseudouridine (Ψ) is the most abundant post-transcriptionally modified ribonucleoside. Different Ψ modifications correlate with stress responses and are postulated to coordinate the distinct biological responses to a diverse panel of cellular stresses. With the help of different guide RNAs, the dyskerin complex pseudouridylates ribosomal RNA, small nuclear RNA and selective messenger RNAs. To monitor Ψ levels quantitatively, a previously reported high performance liquid chromatography method coupled with ultraviolet detection (HPLC-UV) was modified to determine total Ψ levels in different cellular RNA fractions. Our method was validated to be accurate and precise within the linear range of 0.06–15.36 pmol/μL and to have absolute Ψ quantification levels as low as 3.07 pmol. Using our optimized HPLC assay, we found that 1.20% and 1.94% of all ribonucleosides in nuclear-enriched RNA and small non-coding RNA pools from the HEK293 cell line, and 1.77% and 0.98% of ribonucleosides in 18S and 28S rRNA isolated from the HeLa cell line, were pseudouridylated. Upon knockdown of dyskerin expression, a consistent and significant reduction in total Ψ levels in nuclear-enriched RNA pools was observed. Our assay provides a fast and accurate quantification method to measure changes in Ψ levels of different RNA pools without sample derivatization.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 19
    Publikationsdatum: 2017-09-07
    Beschreibung: Genes, Vol. 8, Pages 222: RECQ1 Helicase Silencing Decreases the Tumour Growth Rate of U87 Glioblastoma Cell Xenografts in Zebrafish Embryos Genes doi: 10.3390/genes8090222 Authors: Miloš Vittori Barbara Breznik Katja Hrovat Saša Kenig Tamara T. Lah RECQ1 helicase has multiple roles in DNA replication, including restoration of the replication fork and DNA repair, and plays an important role in tumour progression. Its expression is highly elevated in glioblastoma as compared to healthy brain tissue. We studied the effects of small hairpin RNA (shRNA)-induced silencing of RECQ1 helicase on the increase in cell number and the invasion of U87 glioblastoma cells. RECQ1 silencing reduced the rate of increase in the number of U87 cells by 30%. This corresponded with a 40% reduction of the percentage of cells in the G2 phase of the cell cycle, and an accumulation of cells in the G1 phase. These effects were confirmed in vivo, in the brain of zebrafish (Danio rerio) embryos, by implanting DsRed-labelled RECQ1 helicase-silenced and control U87 cells. The growth of resulting tumours was quantified by monitoring the increase in xenograft fluorescence intensity during a three-day period with fluorescence microscopy. The reduced rate of tumour growth, by approximately 30% in RECQ1 helicase-silenced cells, was in line with in vitro measurements of the increase in cell number upon RECQ1 helicase silencing. However, RECQ1 helicase silencing did not affect invasive behaviour of U87 cells in the zebrafish brain. This is the first in vivo confirmation that RECQ1 helicase is a promising molecular target in the treatment of glioblastoma.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 20
    Publikationsdatum: 2017-09-07
    Beschreibung: Genes, Vol. 8, Pages 221: High-Throughput Study of the Effects of Celastrol on Activated Fibroblast-Like Synoviocytes from Patients with Rheumatoid Arthritis Genes doi: 10.3390/genes8090221 Authors: Zhengyu Fang Dongyi He Bo Yu Feng Liu Jianping Zuo Yuxia Li Qi Lin Xiaodong Zhou Qingwen Wang Celastrol, a natural triterpene, exhibits potential anti-inflammatory activity in a variety of inflammatory diseases. The present study aimed to investigate its biological effect on activated fibroblast-like synoviocytes (FLSs) from patients with rheumatoid arthritis (RA). The primary FLSs of the synovial tissues were obtained from synovial biopsies of patients with RA. The normal human FLS line (HFLS) was used as a control. After the RA–FLSs and HFLSs were treated with or without celastrol, various approaches, including the WST-1 assay, transwell assay, real-time PCR and ELISA analysis, were performed to estimate proliferation, invasion and expression of pro-inflammatory cytokines of the RA–FLSs. Microarray analysis was performed to screen for differentially expressed genes in RA–FLSs before and after celastrol treatment. The results showed that treatment of celastrol attenuated both the proliferation and invasion of the RA–FLSs. The expression of several chemokine genes, including CCL2, CXCL10, CXCL12, CCR2 and CXCR4, was significantly changed after celastrol treatment. The genes involved in the NF-κB signaling pathway appeared to be regulated by celastrol.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 21
    Publikationsdatum: 2017-09-19
    Beschreibung: Genes, Vol. 8, Pages 226: Salt-Stress Response Mechanisms Using de Novo Transcriptome Sequencing of Salt-Tolerant and Sensitive Corchorus spp. Genotypes Genes doi: 10.3390/genes8090226 Authors: Zemao Yang Ruike Lu Zhigang Dai An Yan Qing Tang Chaohua Cheng Ying Xu Wenting Yang Jianguang Su High salinity is a major environmental stressor for crops. To understand the regulatory mechanisms underlying salt tolerance, we conducted a comparative transcriptome analysis between salt-tolerant and salt-sensitive jute (Corchorus spp.) genotypes in leaf and root tissues under salt stress and control conditions. In total, 68,961 unigenes were identified. Additionally, 11,100 unigenes (including 385 transcription factors (TFs)) exhibited significant differential expression in salt-tolerant or salt-sensitive genotypes. Numerous common and unique differentially expressed unigenes (DEGs) between the two genotypes were discovered. Fewer DEGs were observed in salt-tolerant jute genotypes whether in root or leaf tissues. These DEGs were involved in various pathways, such as ABA signaling, amino acid metabolism, etc. Among the enriched pathways, plant hormone signal transduction (ko04075) and cysteine/methionine metabolism (ko00270) were the most notable. Eight common DEGs across both tissues and genotypes with similar expression profiles were part of the PYL-ABA-PP2C (pyrabactin resistant-like/regulatory components of ABA receptors-abscisic acid-protein phosphatase 2C). The methionine metabolism pathway was only enriched in salt-tolerant jute root tissue. Twenty-three DEGs were involved in methionine metabolism. Overall, numerous common and unique salt-stress response DEGs and pathways between salt-tolerant and salt-sensitive jute have been discovered, which will provide valuable information regarding salt-stress response mechanisms and help improve salt-resistance molecular breeding in jute.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 22
    Publikationsdatum: 2017-09-19
    Beschreibung: Genes, Vol. 8, Pages 232: Effects of Cellular Methylation on Transgene Expression and Site-Specific Integration of Adeno-Associated Virus Genes doi: 10.3390/genes8090232 Authors: Diptiman Chanda Jonathan Hensel Jerome Higgs Rajat Grover Niroop Kaza Selvarangan Ponnazhagan DNA methylation is a major epigenetic event that affects not only cellular gene expression but that also has the potential to influence bacterial and viral DNA in their host-dependent functions. Adeno-associated virus (AAV) genome contains a high degree of CpG sequences capable of methylation in its terminal repeat sequences, which are the sole elements retained in AAV-based vectors used in gene therapy. The present study determined the influence of methylation status of the host cell on wild type (wt) AAV integration and recombinant (r) AAV transgene expression in HeLa cells. Results of the study indicated that hypo-methylation significantly enhanced both wtAAV chromosomal integration and transgene expression of rAAV. A direct influence of methylation on AAV integration was further confirmed by methylating the AAVS1 integration sites prior to viral infection with DNA trans-complementation assay. These results signify the importance of epigenetic status of target cells as one of the key factors in long-term transgene expression in AAV gene therapy.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 23
    Publikationsdatum: 2017-09-19
    Beschreibung: Genes, Vol. 8, Pages 233: Predicting Variation of DNA Shape Preferences in Protein-DNA Interaction in Cancer Cells with a New Biophysical Model Genes doi: 10.3390/genes8090233 Authors: Kirill Batmanov Junbai Wang DNA shape readout is an important mechanism of transcription factor target site recognition, in addition to the sequence readout. Several machine learning-based models of transcription factor–DNA interactions, considering DNA shape features, have been developed in recent years. Here, we present a new biophysical model of protein–DNA interactions by integrating the DNA shape properties. It is based on the neighbor dinucleotide dependency model BayesPI2, where new parameters are restricted to a subspace spanned by the dinucleotide form of DNA shape features. This allows a biophysical interpretation of the new parameters as a position-dependent preference towards specific DNA shape features. Using the new model, we explore the variation of DNA shape preferences in several transcription factors across various cancer cell lines and cellular conditions. The results reveal that there are DNA shape variations at FOXA1 (Forkhead Box Protein A1) binding sites in steroid-treated MCF7 cells. The new biophysical model is useful for elucidating the finer details of transcription factor–DNA interaction, as well as for predicting cancer mutation effects in the future.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 24
    facet.materialart.
    Unbekannt
    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publikationsdatum: 2017-08-16
    Beschreibung: Genes, Vol. 8, Pages 201: Mutation Clusters from Cancer Exome Genes doi: 10.3390/genes8080201 Authors: Zura Kakushadze Willie Yu We apply our statistically deterministic machine learning/clustering algorithm *K-means (recently developed in https://ssrn.com/abstract=2908286) to 10,656 published exome samples for 32 cancer types. A majority of cancer types exhibit a mutation clustering structure. Our results are in-sample stable. They are also out-of-sample stable when applied to 1389 published genome samples across 14 cancer types. In contrast, we find in- and out-of-sample instabilities in cancer signatures extracted from exome samples via nonnegative matrix factorization (NMF), a computationally-costly and non-deterministic method. Extracting stable mutation structures from exome data could have important implications for speed and cost, which are critical for early-stage cancer diagnostics, such as novel blood-test methods currently in development.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 25
    Publikationsdatum: 2017-08-17
    Beschreibung: Genes, Vol. 8, Pages 194: Distribution of FMR1 and FMR2 Repeats in Argentinean Patients with Primary Ovarian Insufficiency Genes doi: 10.3390/genes8080194 Authors: Lucía Espeche Violeta Chiauzzi Ianina Ferder Mehrnoosh Arrar Andrea Solari Carlos Bruque Marisol Delea Susana Belli Cecilia Fernández Noemí Buzzalino Eduardo Charreau Liliana Dain The premutation state of FMR1 (Fragile X Mental Retardation 1) has been associated with primary ovarian insufficiency (POI), and is the most common known genetic cause for 46,XX patients. Nevertheless, very few studies have analyzed its frequency in Latin American populations. Additionally, a relationship between alleles carrying a cryptic microdeletion in the 5’UTR of FMR2 and the onset of POI has only been studied in one population. Our aim was to analyze the incidence of FMR1 premutations and putative microdeletions in exon 1 of FMR2 in a cohort of Argentinean women with POI. We studied 133 patients and 84 controls. Fluorescent PCR was performed, and the FMR2 exon 1 was further sequenced in samples presenting less than 11 repeats. We found the frequency of FMR1 premutations to be 6.7% and 2.9% for familial and sporadic patients, respectively. Among controls, 1/84 women presented a premutation. In addition, although we did not find microdeletions in FMR2, we observed a change (T >C) adjacent to the repeats in two sisters with POI. Given the repetitive nature of the sequence involved, we could not ascertain whether this represents a single nucleotide polymorphism (SNP) or a deletion. Therefore, a relationship between FMR2 and POI could not be established for our population.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 26
    Publikationsdatum: 2017-08-22
    Beschreibung: Multi-sectoral partnerships (MSPs) form an increasingly popular and important part of the global climate and disaster risk governance landscape, but literature offers little critical investigation of this phenomenon. In particular it remains unclear how MSPs can support the transition from agenda-setting to implementation in response to multiple current and future pressures threatening the resilience of cities. Through the lens of the London Climate Change Partnership (LCCP) and drawing from other MSP examples, this paper investigates the scope for MSPs to enhance climate adaptation in an urban context. Our paper has two main aims: to expand understanding of the role of MSPs in the adaptation decision process in the context of the wider governance literature, and to shed some light on the complexities of transitioning through that process. To clarify the role of a MSP we propose a distinction between ‘first generation’ and ‘second generation’ MSPs, illustrating the progression from agenda-setting to implementation: ‘first generation’ MSPs are focused on agenda-setting and knowledge sharing in order to support decision-makers, while ‘second generation’ partnerships are aimed at implementing solutions. We consider this distinction from the perspective of the individual members and their perceptions, motivations and expectations. We find that the dynamic nature of urban adaptation with a shifting focus from initial agenda setting towards the implementation of actions presents challenges for existing MSPs, particularly such long-established ones like the LCCP. Our investigation shows that ‘first generation’ MSPs can play important roles in agenda-setting, but finds little evidence of ‘second generation’ MSPs achieving implementation.
    Digitale ISSN: 2328-4277
    Thema: Geologie und Paläontologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 27
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    Unbekannt
    American Geophysical Union (AGU)
    Publikationsdatum: 2017-08-22
    Beschreibung: Improving society's ability to prepare for, respond to and recover from flooding requires integrated, anticipatory flood risk management (FRM) . However, most countries still focus their efforts on responding to flooding events if and when they occur rather than addressing their current and future vulnerability to flooding. Flood insurance is one mechanism that could a more ex-ante approach to risk by supporting risk reduction activities. This paper uses an adapted version of Easton's System Theory to investigate the role of insurance for FRM in Germany and England. We introduce an anticipatory FRM framework, which allows to consider flood insurance as part of a broader policy field. We analyse if and how flood insurance can catalyse a change towards a more anticipatory approach to FRM. In particular we consider insurance's role in influencing five key components of an anticipatory FRM: risk knowledge, prevention through better planning, property-level protection measures, structural protection and preparedness (for response). We find that in both countries FRM is still a reactive, event-driven process, while anticipatory FRM remains underdeveloped. However, collaboration between insurers and FRM decision-makers has already been successful, for example in improving risk knowledge and awareness, while in other areas insurance acts as a disincentive for more risk reduction action. In both countries there is evidence that insurance can play a significant role in encouraging anticipatory FRM, but this remains underutilized. Effective collaboration between insurers and government, should not be seen as a cost, but as an investment to secure future insurability through flood resilience.
    Digitale ISSN: 2328-4277
    Thema: Geologie und Paläontologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 28
    Publikationsdatum: 2017-08-23
    Beschreibung: Genes, Vol. 8, Pages 208: A Rare Form of Retinal Dystrophy Caused by Hypomorphic Nonsense Mutations in CEP290 Genes doi: 10.3390/genes8080208 Authors: Susanne Roosing Frans Cremers Frans Riemslag Marijke Zonneveld-Vrieling Herman Talsma Francoise Klessens-Godfroy Anneke den Hollander L. van den Born Purpose: To identify the gene defect and to study the clinical characteristics and natural course of disease in a family originally diagnosed with oligocone trichromacy (OT), a rare congenital cone dysfunction syndrome. Methods: Extensive clinical and ophthalmologic assessment was performed on two siblings with OT and long-term follow up data were analyzed. Subsequently, whole exome sequencing (WES) and Sanger sequence analysis of CEP290 was performed in the two siblings. Additionally, the identified CEP290 mutations were analyzed in persons with achromatopsia (ACHM) (n = 23) and autosomal recessive or isolated cone dystrophy (CD; n = 145). Results: In the first decade of life, the siblings were diagnosed with OT based on low visual acuity, photophobia, nystagmus, and absent cone response on electroretinography , but with normal color discrimination. Over time, the phenotype of OT evolved to a progressive degenerative disease without any CEP290-associated non-ocular features. In both siblings, two nonsense mutations (c.451C>T; p.(Arg151*) and c.4723A>T; p.(Lys1575*)) in CEP290 were found. Previously, p.(Arg151*) was demonstrated to induce nonsense-mediated alternative splicing events leading to intact open reading frames of the resulting mRNA products (p.(Leu148_Glu165del) and p.(Leu148_Lys172del)). mRNA analysis for p.(Lys1575*) confirmed a suspected hypomorphic character, as exon 36 skipping was observed in a small fraction of CEP290 mRNA, resulting in a 36 aa in-frame deletion (p.(Glu1569_Trp1604del)). No additional cases carrying these variants were identified in the ACHM and CD cohorts. Conclusions: Compound heterozygous hypomorphic mutations in CEP290 may lead to a rare form of cone-dominated retinal dystrophy, a novel phenotype belonging to the CEP290-associated spectrum of ciliopathies. These findings provide insight into the effect of CEP290 mutations on the clinical phenotype.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 29
    facet.materialart.
    Unbekannt
    American Geophysical Union (AGU)
    Publikationsdatum: 2017-08-30
    Beschreibung: Just as carbon fueled the Industrial Revolution, nitrogen has fueled an Agricultural Revolution. The use of synthetic nitrogen fertilizers and the cultivation of nitrogen-fixing crops both expanded exponentially during the last century, with most of the increase occurring after 1960. As a result, the current flux of reactive, or fixed, nitrogen compounds to the biosphere due to human activities is roughly equivalent to the total flux of fixed nitrogen from all natural sources, both on land masses and in the world's oceans. Natural fluxes of fixed nitrogen are subject to very large uncertainties, but anthropogenic production of reactive nitrogen has increased almost five-fold in the last half-century, and this rapid increase in anthropogenic fixed nitrogen has removed any uncertainty on the relative importance of anthropogenic fluxes to the natural budget. The increased use of nitrogen has been critical for increased crop yields and protein production needed to keep pace with the growing world population. However, similar to carbon, the release of fixed nitrogen into the natural environment is linked to adverse consequences at local, regional, and global scales. Anthropogenic contributions of fixed nitrogen continue to grow relative to the natural budget, with uncertain consequences.
    Digitale ISSN: 2328-4277
    Thema: Geologie und Paläontologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 30
    Publikationsdatum: 2017-08-30
    Beschreibung: Genes, Vol. 8, Pages 213: 5′-UTR and 3′-UTR Regulation of MICB Expression in Human Cancer Cells by Novel microRNAs Genes doi: 10.3390/genes8090213 Authors: Wipaporn Wongfieng Amonrat Jumnainsong Yaovalux Chamgramol Banchob Sripa Chanvit Leelayuwat The treatment of cancer through the induction of natural killer group 2, member D (NKG2D) ligands is of interest, but understanding of mechanisms controlling expression of individual ligand is limited. The major histocompatibility complex (MHC) class I chain related protein B (MICB) is a member of NKG2D ligands. We aimed to investigate the role of 3′-untranslated (3′-UTR) and 5′-untranslated regions (5′-UTR) in post-transcriptional regulation of MICB. Nine novel microRNAs (miRNAs) predicted to interact with 3′-UTR and 5′-UTR using TargetScan, RNAhybrid and miBridge were identified. Their regulation of 3′-UTR, 5′-UTR and both 3′- and 5′-UTR sequences of MICB were indicated by the reduction of luciferase activities of luciferase reporter constructs. Mutations of miRNA binding sites at 3′- and 5′-UTRs resulted in increased luciferase activities confirming the regulation of nine candidate miRNAs. In addition, overexpression of candidate miRNAs also down-regulated the expression of reporter constructs. Consequently, the overexpression and inhibition of candidate miRNAs lead to the decreased and increased. MICB protein expressions on the cells tested, respectively. This study has identified a new role of miRNAs in regulation of MICB expression via both 3′-UTR and 5′-UTR sequences applicable for cancer immunotherapy.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 31
    Publikationsdatum: 2017-08-31
    Beschreibung: Genes, Vol. 8, Pages 215: Intrachromosomal Rearrangements in Rodents from the Perspective of Comparative Region-Specific Painting Genes doi: 10.3390/genes8090215 Authors: Svetlana Romanenko Natalya Serdyukova Polina Perelman Svetlana Pavlova Nina Bulatova Feodor Golenishchev Roscoe Stanyon Alexander Graphodatsky It has long been hypothesized that chromosomal rearrangements play a central role in different evolutionary processes, particularly in speciation and adaptation. Interchromosomal rearrangements have been extensively mapped using chromosome painting. However, intrachromosomal rearrangements have only been described using molecular cytogenetics in a limited number of mammals, including a few rodent species. This situation is unfortunate because intrachromosomal rearrangements are more abundant than interchromosomal rearrangements and probably contain essential phylogenomic information. Significant progress in the detection of intrachromosomal rearrangement is now possible, due to recent advances in molecular biology and bioinformatics. We investigated the level of intrachromosomal rearrangement in the Arvicolinae subfamily, a species-rich taxon characterized by very high rate of karyotype evolution. We made a set of region specific probes by microdissection for a single syntenic region represented by the p-arm of chromosome 1 of Alexandromys oeconomus, and hybridized the probes onto the chromosomes of four arvicolines (Microtus agrestis, Microtus arvalis, Myodes rutilus, and Dicrostonyx torquatus). These experiments allowed us to show the intrachromosomal rearrangements in the subfamily at a significantly higher level of resolution than previously described. We found a number of paracentric inversions in the karyotypes of M. agrestis and M. rutilus, as well as multiple inversions and a centromere shift in the karyotype of M. arvalis. We propose that during karyotype evolution, arvicolines underwent a significant number of complex intrachromosomal rearrangements that were not previously detected.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 32
    Publikationsdatum: 2017-09-09
    Beschreibung: Genes, Vol. 8, Pages 224: Functional Characterization of Selected Universal Stress Protein from Salvia miltiorrhiza (SmUSP) in Escherichia coli Genes doi: 10.3390/genes8090224 Authors: Xiao-Fan Wang Jiao Su Na Yang Hui Zhang Xiao-Yan Cao Jie-Fang Kang The multigene universal stress protein (USP) family is evolutionarily conserved. Members play indispensable roles in plant tolerance to abiotic stresses. Although relatively well-characterized in model plants, such as Arabidopsis thaliana and Oryza sativa, this family has not been investigated in Salvia miltiorrhiza, an important herbal plant for which yields can be limited by various abiotic stresses. Here, we identified 32 USP family members in the S. miltiorrhiza genome, and used phylogenetic analysis to sort these SmUSPs into four groups. Groups A and B belong to the ATP-binding class whereas Groups C and D are in the non-ATP-binding class. Motif analysis and multiple sequence alignment hinted that members of group A and B were able to bind ATP. Our qRT-PCR data from different tissues/organs and under salt and heat stresses provided an overall expression pattern for those genes. Three SmUSPs (SmUSP1, SmUSP8, and SmUSP27) were cloned from S. miltiorrhiza and functionally characterized in Escherichia coli. Compared with the control cells, those that expressed SmUSPs exhibited enhanced tolerance to salt, heat, and a combination of the two. This suggested that the protein has a protective role in cells when exposed to single-stress and multiple-stress conditions. Our findings provide valuable information that helps improve our understanding of the evolutionary and functional conservation and diversity associated with the USP gene family in S. miltiorrhiza.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 33
    Publikationsdatum: 2017-09-09
    Beschreibung: Genes, Vol. 8, Pages 223: Advances in Genomic Profiling and Analysis of 3D Chromatin Structure and Interaction Genes doi: 10.3390/genes8090223 Authors: Binhua Tang Xiaolong Cheng Yunlong Xi Zixin Chen Yufan Zhou Victor Jin Recent sequence-based profiling technologies such as high-throughput sequencing to detect fragment nucleotide sequence (Hi-C) and chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) have revolutionized the field of three-dimensional (3D) chromatin architecture. It is now recognized that human genome functions as folded 3D chromatin units and looping paradigm is the basic principle of gene regulation. To better interpret the 3D data dramatically accumulating in past five years and to gain deep biological insights, huge efforts have been made in developing novel quantitative analysis methods. However, the full understanding of genome regulation requires thorough knowledge in both genomic technologies and their related data analyses. We summarize the recent advances in genomic technologies in identifying the 3D chromatin structure and interaction, and illustrate the quantitative analysis methods to infer functional domains and chromatin interactions, and further elucidate the emerging single-cell Hi-C technique and its computational analysis, and finally discuss the future directions such as advances of 3D chromatin techniques in diseases.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 34
    Publikationsdatum: 2017-09-13
    Beschreibung: Land surface albedo is a key parameter controlling the local energy budget, and altering the albedo of built surfaces has been proposed as a tool to mitigate high near-surface temperatures in the Urban Heat Island. However, most research on albedo in urban landscapes has used coarse-resolution data, and few studies have attempted to relate albedo to other urban land cover characteristics. This study provides an empirical description of urban summertime albedo using 30 m remote sensing measurements in the metropolitan area around Boston, Massachusetts, relating albedo to metrics of impervious cover fraction, tree canopy coverage, population density, and land surface temperature (LST). At 30 m spatial resolution, median albedo over the study area (excluding open water) was 0.152 (0.112–0.187). Trends of lower albedo with increasing urbanization metrics and temperature emerged only after aggregating data to 500 m or the boundaries of individual towns, at which scale a −0.01 change in albedo was associated with a 29 (25–35)% decrease in canopy cover, a 27 (24–30)% increase in impervious cover, and an increase in population from 11–386 km −2 . The most intensively urbanized towns in the region showed albedo up to 0.035 lower than the least urbanized towns, and mean mid-morning LST 12.6 °C higher. Trends in albedo derived from 500 m MODIS measurements were comparable, but indicated a strong contribution of open water at this coarser resolution. These results reveal linkages between albedo and urban land cover character, and offer empirical context for climate resilient planning and future landscape functional changes with urbanization.
    Digitale ISSN: 2328-4277
    Thema: Geologie und Paläontologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 35
    Publikationsdatum: 2017-09-16
    Beschreibung: Genes, Vol. 8, Pages 228: Isoform Sequencing Provides a More Comprehensive View of the Panax ginseng Transcriptome Genes doi: 10.3390/genes8090228 Authors: Ick-Hyun Jo Jinsu Lee Chi Hong Dong Lee Wonsil Bae Sin-Gi Park Yong Ahn Young Kim Jang Kim Jung Lee Dong Hyun Sung-Keun Rhee Chang Hong Kyong Bang Hojin Ryu Korean ginseng (Panax ginseng C.A. Meyer) has been widely used for medicinal purposes and contains potent plant secondary metabolites, including ginsenosides. To obtain transcriptomic data that offers a more comprehensive view of functional genomics in P. ginseng, we generated genome-wide transcriptome data from four different P. ginseng tissues using PacBio isoform sequencing (Iso-Seq) technology. A total of 135,317 assembled transcripts were generated with an average length of 3.2 kb and high assembly completeness. Of those unigenes, 67.5% were predicted to be complete full-length (FL) open reading frames (ORFs) and exhibited a high gene annotation rate. Furthermore, we successfully identified unique full-length genes involved in triterpenoid saponin synthesis and plant hormonal signaling pathways, including auxin and cytokinin. Studies on the functional genomics of P. ginseng seedlings have confirmed the rapid upregulation of negative feed-back loops by auxin and cytokinin signaling cues. The conserved evolutionary mechanisms in the auxin and cytokinin canonical signaling pathways of P. ginseng are more complex than those in Arabidopsis thaliana. Our analysis also revealed a more detailed view of transcriptome-wide alternative isoforms for 88 genes. Finally, transposable elements (TEs) were also identified, suggesting transcriptional activity of TEs in P. ginseng. In conclusion, our results suggest that long-read, full-length or partial-unigene data with high-quality assemblies are invaluable resources as transcriptomic references in P. ginseng and can be used for comparative analyses in closely related medicinal plants.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 36
    Publikationsdatum: 2017-09-21
    Beschreibung: Genes, Vol. 8, Pages 236: Zebrafish in Translational Cancer Research: Insight into Leukemia, Melanoma, Glioma and Endocrine Tumor Biology Genes doi: 10.3390/genes8090236 Authors: Aurora Idilli Francesca Precazzini Maria Mione Viviana Anelli Over the past 15 years, zebrafish have emerged as a powerful tool for studying human cancers. Transgenic techniques have been employed to model different types of tumors, including leukemia, melanoma, glioblastoma and endocrine tumors. These models present histopathological and molecular conservation with their human cancer counterparts and have been fundamental for understanding mechanisms of tumor initiation and progression. Moreover, xenotransplantation of human cancer cells in embryos or adult zebrafish offers the advantage of studying the behavior of human cancer cells in a live organism. Chemical-genetic screens using zebrafish embryos have uncovered novel druggable pathways and new therapeutic strategies, some of which are now tested in clinical trials. In this review, we will report on recent advances in using zebrafish as a model in cancer studies—with specific focus on four cancer types—where zebrafish has contributed to novel discoveries or approaches to novel therapies.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 37
    Publikationsdatum: 2017-09-22
    Beschreibung: Genes, Vol. 8, Pages 237: Optimized mtDNA Control Region Primer Extension Capture Analysis for Forensically Relevant Samples and Highly Compromised mtDNA of Different Age and Origin Genes doi: 10.3390/genes8100237 Authors: Mayra Eduardoff Catarina Xavier Christina Strobl Andrea Casas-Vargas Walther Parson The analysis of mitochondrial DNA (mtDNA) has proven useful in forensic genetics and ancient DNA (aDNA) studies, where specimens are often highly compromised and DNA quality and quantity are low. In forensic genetics, the mtDNA control region (CR) is commonly sequenced using established Sanger-type Sequencing (STS) protocols involving fragment sizes down to approximately 150 base pairs (bp). Recent developments include Massively Parallel Sequencing (MPS) of (multiplex) PCR-generated libraries using the same amplicon sizes. Molecular genetic studies on archaeological remains that harbor more degraded aDNA have pioneered alternative approaches to target mtDNA, such as capture hybridization and primer extension capture (PEC) methods followed by MPS. These assays target smaller mtDNA fragment sizes (down to 50 bp or less), and have proven to be substantially more successful in obtaining useful mtDNA sequences from these samples compared to electrophoretic methods. Here, we present the modification and optimization of a PEC method, earlier developed for sequencing the Neanderthal mitochondrial genome, with forensic applications in mind. Our approach was designed for a more sensitive enrichment of the mtDNA CR in a single tube assay and short laboratory turnaround times, thus complying with forensic practices. We characterized the method using sheared, high quantity mtDNA (six samples), and tested challenging forensic samples (n = 2) as well as compromised solid tissue samples (n = 15) up to 8 kyrs of age. The PEC MPS method produced reliable and plausible mtDNA haplotypes that were useful in the forensic context. It yielded plausible data in samples that did not provide results with STS and other MPS techniques. We addressed the issue of contamination by including four generations of negative controls, and discuss the results in the forensic context. We finally offer perspectives for future research to enable the validation and accreditation of the PEC MPS method for final implementation in forensic genetic laboratories.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 38
    Publikationsdatum: 2017-09-14
    Beschreibung: Genes, Vol. 8, Pages 227: The Chloroplast Genome Sequence of Scutellaria baicalensis Provides Insight into Intraspecific and Interspecific Chloroplast Genome Diversity in Scutellaria Genes doi: 10.3390/genes8090227 Authors: Dan Jiang Zhenyu Zhao Teng Zhang Wenhao Zhong Chunsheng Liu Qingjun Yuan Luqi Huang Scutellaria baicalensis Georgi (Lamiaceae) is the source of the well-known traditional Chinese medicine “HuangQin” (Radix Scutellariae). Natural sources of S. baicalensis are rapidly declining due to high market demand and overexploitation. Moreover, the commercial products of Radix Scutellariae have often been found to contain adulterants in recent years, which may give rise to issues regarding drug efficacy and safety. In this study, we developed valuable chloroplast molecular resources by comparing intraspecific and interspecific chloroplast genome. The S. baicalensis chloroplast genome is a circular molecule consisting of two single-copy regions separated by a pair of inverted repeats. Comparative analyses of three Scutellaria chloroplast genomes revealed six variable regions (trnH-psbA, trnK-rps16, petN-psbM, trnT-trnL, petA-psbJ, and ycf1) that could be used as DNA barcodes. There were 25 single nucleotide polymorphisms(SNPs) and 29 indels between the two S. baicalensis genotypes. All of the indels occurred within non-coding regions. Phylogenetic analysis suggested that Scutellarioideae is a sister taxon to Lamioideae. These resources could be used to explore the variation present in Scutellaria populations and for further evolutionary, phylogenetic, barcoding and genetic engineering studies, in addition to effective exploration and conservation of S. baicalensis.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 39
    Publikationsdatum: 2017-09-14
    Beschreibung: Genes, Vol. 8, Pages 225: Identification of the Ovine Keratin-Associated Protein 26-1 Gene and Its Association with Variation in Wool Traits Genes doi: 10.3390/genes8090225 Authors: Shaobin Li Huitong Zhou Hua Gong Fangfang Zhao Jiang Hu Yuzhu Luo Jon Hickford Keratin-associated proteins (KAPs) are structural components of wool and hair fibres, and are believed to play a role in defining the physico-mechanical properties of the wool fibre. In this study, the putative ovine homologue of the human KAP26-1 gene (KRTAP26-1) was sequenced and four variants (named A–D) were identified. The sequences shared some identity with each other and with other KRTAPs, but they had the greatest similarity with the human KRTAP26-1 sequence. This suggests they represent different variants of ovine KRTAP26-1. The association of these KRTAP26-1 variants with wool traits was investigated in the 383 Merino-Southdown cross sheep. The presence of B was associated (p < 0.05) with an increase in mean fibre diameter (MFD), mean fibre curvature, and prickle factor (PF). The presence of C was found to be associated (p < 0.05) with an increase in wool yield (Yield) and mean staple length (MSL), and a decrease in MFD, fibre diameter standard deviation (FDSD), and PF. The results suggest that sheep with C have, on average, higher wool quality. These results may be useful in the future development of breeding programs based on decreasing wool MFD and FDSD, or on increasing wool MSL.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 40
    Publikationsdatum: 2017-09-16
    Beschreibung: Genes, Vol. 8, Pages 229: Emerging Estrogenic Pollutants in the Aquatic Environment and Breast Cancer Genes doi: 10.3390/genes8090229 Authors: Sylvain Lecomte Denis Habauzit Thierry Charlier Farzad Pakdel The number and amount of man-made chemicals present in the aquatic environment has increased considerably over the past 50 years. Among these contaminants, endocrine-disrupting chemicals (EDCs) represent a significant proportion. This family of compounds interferes with normal hormonal processes through multiple molecular pathways. They represent a potential risk for human and wildlife as they are suspected to be involved in the development of diseases including, but not limited to, reprotoxicity, metabolic disorders, and cancers. More precisely, several studies have suggested that the increase of breast cancers in industrialized countries is linked to exposure to EDCs, particularly estrogen-like compounds. Estrogen receptors alpha (ERα) and beta (ERβ) are the two main transducers of estrogen action and therefore important targets for these estrogen-like endocrine disrupters. More than 70% of human breast cancers are ERα-positive and estrogen-dependent, and their development and growth are not only influenced by endogenous estrogens but also likely by environmental estrogen-like endocrine disrupters. It is, therefore, of major importance to characterize the potential estrogenic activity from contaminated surface water and identify the molecules responsible for the hormonal effects. This information will help us understand how environmental contaminants can potentially impact the development of breast cancer and allow us to fix a maximal limit to the concentration of estrogen-like compounds that should be found in the environment. The aim of this review is to provide an overview of emerging estrogen-like compounds in the environment, sum up studies demonstrating their direct or indirect interactions with ERs, and link their presence to the development of breast cancer. Finally, we emphasize the use of in vitro and in vivo methods based on the zebrafish model to identify and characterize environmental estrogens.
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  • 41
    Publikationsdatum: 2017-09-19
    Beschreibung: Genes, Vol. 8, Pages 231: Transcription Factors Responding to Pb Stress in Maize Genes doi: 10.3390/genes8090231 Authors: Yanling Zhang Fei Ge Fengxia Hou Wenting Sun Qi Zheng Xiaoxiang Zhang Langlang Ma Jun Fu Xiujing He Huanwei Peng Guangtang Pan Yaou Shen Pb can damage the physiological function of human organs by entering the human body via food-chain enrichment. Revealing the mechanisms of maize tolerance to Pb is critical for preventing this. In this study, a Pb-tolerant maize inbred line, 178, was used to analyse transcription factors (TFs) expressed under Pb stress based on RNA sequencing data. A total of 464 genes expressed in control check (CK) or Pb treatment samples were annotated as TFs. Among them, 262 differentially expressed transcription factors (DETs) were identified that responded to Pb treatment. Furthermore, the DETs were classified into 4 classes according to their expression patterns, and 17, 12 and 2 DETs were significantly annotated to plant hormone signal transduction, basal transcription factors and base excision repair, respectively. Seventeen DETs were found to participate in the plant hormone signal transduction pathway, where basic leucine zippers (bZIPs) were the most significantly enriched TFs, with 12 members involved. We further obtained 5 Arabidopsis transfer DNA (T-DNA) mutants for 6 of the maize bZIPs, among which the mutants atbzip20 and atbzip47, representing ZmbZIP54 and ZmbZIP107, showed obviously inhibited growth of roots and above-ground parts, compared with wild type. Five highly Pb-tolerant and 5 highly Pb-sensitive in maize lines were subjected to DNA polymorphism and expression level analysis of ZmbZIP54 and ZmbZIP107. The results suggested that differences in bZIPs expression partially accounted for the differences in Pb-tolerance among the maize lines. Our results contribute to the understanding of the molecular regulation mechanisms of TFs in maize under Pb stress.
    Digitale ISSN: 2073-4425
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  • 42
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    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publikationsdatum: 2017-09-19
    Beschreibung: Genes, Vol. 8, Pages 230: Satellite DNA: An Evolving Topic Genes doi: 10.3390/genes8090230 Authors: Manuel Garrido-Ramos Satellite DNA represents one of the most fascinating parts of the repetitive fraction of the eukaryotic genome. Since the discovery of highly repetitive tandem DNA in the 1960s, a lot of literature has extensively covered various topics related to the structure, organization, function, and evolution of such sequences. Today, with the advent of genomic tools, the study of satellite DNA has regained a great interest. Thus, Next-Generation Sequencing (NGS), together with high-throughput in silico analysis of the information contained in NGS reads, has revolutionized the analysis of the repetitive fraction of the eukaryotic genomes. The whole of the historical and current approaches to the topic gives us a broad view of the function and evolution of satellite DNA and its role in chromosomal evolution. Currently, we have extensive information on the molecular, chromosomal, biological, and population factors that affect the evolutionary fate of satellite DNA, knowledge that gives rise to a series of hypotheses that get on well with each other about the origin, spreading, and evolution of satellite DNA. In this paper, I review these hypotheses from a methodological, conceptual, and historical perspective and frame them in the context of chromosomal organization and evolution.
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  • 43
    Publikationsdatum: 2017-09-20
    Beschreibung: Genes, Vol. 8, Pages 235: Genome-Wide Analysis of the Biosynthesis and Deactivation of Gibberellin-Dioxygenases Gene Family in Camellia sinensis (L.) O. Kuntze Genes doi: 10.3390/genes8090235 Authors: Cheng Pan Kunhong Tian Qiuyan Ban Leigang Wang Qilu Sun Yan He Yuanfei Yang Yuting Pan Yeyun Li Jiayue Jiang Changjun Jiang Gibberellins (GAs), a class of diterpenoid phytohormones, play a key role in regulating diverse processes throughout the life cycle of plants. Bioactive GA levels are rapidly regulated by Gibberellin-dioxygenases (GAox), which are involved in the biosynthesis and deactivation of gibberellin. In this manuscript, a comprehensive genome-wide analysis was carried out to find all GAox in Camellia sinensis. For the first time in a tea plant, 14 CsGAox genes, containing two domains, DIOX_N (PF14226) and 2OG-FeII_Oxy, were identified (PF03171). These genes all belong to 2-oxoglutarate-dependent dioxygenases (2-ODD), including four CsGA20ox (EC: 1.14.11.12), three CsGA3ox (EC: 1.14.11.15), and seven CsGA2ox (EC: 1.14.11.13). According to the phylogenetic classification as in Arabidopsis, the CsGAox genes spanned five subgroups. Each CsGAox shows tissue-specific expression patterns, although these vary greatly. Some candidate genes, which may play an important role in response to external abiotic stresses, have been identified with regards to patterns, such as CsGA20ox2, CsGA3ox2, CsGA3ox3, CsGA2ox1, CsGA2ox2, and CsGA2ox4. The bioactive GA levels may be closely related to the GA20ox, GA3ox and GA2ox genes. In addition, the candidate genes could be used as marker genes for abiotic stress resistance breeding in tea plants.
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    Thema: Biologie
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  • 44
    Publikationsdatum: 2017-09-20
    Beschreibung: Genes, Vol. 8, Pages 234: Circulating microRNAs and Bioinformatics Tools to Discover Novel Diagnostic Biomarkers of Pediatric Diseases Genes doi: 10.3390/genes8090234 Authors: Antonella Baldassarre Cristina Felli Giorgio Prantera Andrea Masotti MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression at the post-transcriptional level. Current studies have shown that miRNAs are also present in extracellular spaces, packaged into various membrane-bound vesicles, or associated with RNA-binding proteins. Circulating miRNAs are highly stable and can act as intercellular messengers to affect many physiological processes. MicroRNAs circulating in body fluids have generated strong interest in their potential use as clinical biomarkers. In fact, their remarkable stability and the relative ease of detection make circulating miRNAs ideal tools for rapid and non-invasive diagnosis. This review summarizes recent insights about the origin, functions and diagnostic potential of extracellular miRNAs by especially focusing on pediatric diseases in order to explore the feasibility of alternative sampling sources for the development of non-invasive pediatric diagnostics. We will also discuss specific bioinformatics tools and databases for circulating miRNAs focused on the identification and discovery of novel diagnostic biomarkers of pediatric diseases.
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    Thema: Biologie
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  • 45
    Publikationsdatum: 2017-09-20
    Beschreibung: Genes, Vol. 8, Pages 212: Chloroplast Genome Sequence of Clusterbean (Cyamopsis tetragonoloba L.): Genome Structure and Comparative Analysis Genes doi: 10.3390/genes8090212 Authors: Tanvi Kaila Pavan Chaduvla Hukam Rawal Swati Saxena Anshika Tyagi S. Mithra Amolkumar Solanke Pritam Kalia T. Sharma N. Singh Kishor Gaikwad Clusterbean (Cyamopsis tetragonoloba L.), also known as guar, belongs to the family Leguminosae, and is an annual herbaceous legume. Guar is the main source of galactomannan for gas mining industries. In the present study, the draft chloroplast genome of clusterbean was generated and compared to some of the previously reported legume chloroplast genomes. The chloroplast genome of clusterbean is 152,530 bp in length, with a quadripartite structure consisting of large single copy (LSC) and small single copy (SSC) of 83,025 bp and 17,879 bp in size, respectively, and a pair of inverted repeats (IRs) of 25,790 bp in size. The chloroplast genome contains 114 unique genes, which includes 78 protein coding genes, 30 tRNAs, 4 rRNAs genes, and 2 pseudogenes. It also harbors a 50 kb inversion, typical of the Leguminosae family. The IR region of the clusterbean chloroplast genome has undergone an expansion, and hence, the whole rps19 gene is included in the IR, as compared to other legume plastid genomes. A total of 220 simple sequence repeats (SSRs) were detected in the clusterbean plastid genome. The analysis of the clusterbean plastid genome will provide useful insights for evolutionary, molecular and genetic engineering studies.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 46
    Publikationsdatum: 2017-08-12
    Beschreibung: Genes, Vol. 8, Pages 200: Large Introns of 5 to 10 Kilo Base Pairs Can Be Spliced out in Arabidopsis Genes doi: 10.3390/genes8080200 Authors: Ning Chang Qingqing Sun Jinglei Hu Chuanjing An and Hongbo Gao Most of the eukaryotic genes contain introns, which are removed from the pre-RNA during RNA processing. In contrast to the introns in animals, which are usually several kilo base pairs (kb), those in plants generally are very small, which are mostly from dozens of base pairs (bp) to a few hundred bp. According to annotation version 10.0 of the genome of Arabidopsis thaliana, there are 127,854 introns in the nuclear genes; 99.23% of them are less than 1 kb, and only 16 introns are annotated to be larger than 5 kb, which are extremely large introns (ELI) in Arabidopsis. To learn whether these introns are true introns or not and how large introns could be in Arabidopsis, RT-PCR analysis of genes containing these ELIs were carried out. The results indicated that some of these putative introns are indeed ELIs. These ELIs are mainly composed of transposons or transposable elements (TE), excepting one, whose counterparts are also very long in diverse plant species. Thus, this study confirms the existence of introns larger than 5 kb or even 10 kb in Arabidopsis.
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    Thema: Biologie
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  • 47
    Publikationsdatum: 2017-08-11
    Beschreibung: Genes, Vol. 8, Pages 199: Two C3H Type Zinc Finger Protein Genes, CpCZF1 and CpCZF2, from Chimonanthus praecox Affect Stamen Development in Arabidopsis Genes doi: 10.3390/genes8080199 Authors: Huamin Liu Renwei Huang Jing Ma Shunzhao Sui Yulong Guo Daofeng Liu Zhineng Li Yechun Lin Mingyang Li Wintersweet (Chimonanthus praecox) is a popular garden plant because of its flowering time, sweet fragrance, and ornamental value. However, research into the molecular mechanism that regulates flower development in wintersweet is still limited. In this study, we sought to investigate the molecular characteristics, expression patterns, and potential functions of two C3H-type zinc finger (CZF) protein genes, CpCZF1 and CpCZF2, which were isolated from the wintersweet flowers based on the flower developmental transcriptome database. CpCZF1 and CpCZF2 were more highly expressed in flower organs than in vegetative tissues, and during the flower development, their expression profiles were associated with flower primordial differentiation, especially that of petal and stamen primordial differentiation. Overexpression of either CpCZF1 or CpCZF2 caused alterations on stamens in transgenic Arabidopsis. The expression levels of the stamen identity-related genes, such as AGAMOUS (AG), PISTILLATA (PI), SEPALLATA1 (SEP1), SEPALLATA2 (SEP2), SEPALLATA3 (SEP3), APETALA1 (AP1), APETALA2 (AP2), and boundary gene RABBIT EAR (RBE) were significantly up-regulated in CpCZF1 overexpression lines. Additionally, the transcripts of AG, PI, APETALA3 SEP1-3, AP1, and RBE were markedly increased in CpCZF2 overexpressed plant inflorescences. Moreover, CpCZF1 and CpCZF2 could interact with each other by using yeast two-hybrid and bimolecular fluorescence complementation assays. Our results suggest that CpCZF1 and CpCZF2 may be involved in the regulation of stamen development and cause the formation of abnormal flowers in transgenic Arabidopsis plants.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 48
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    American Geophysical Union (AGU)
    Publikationsdatum: 2017-08-18
    Digitale ISSN: 2328-4277
    Thema: Geologie und Paläontologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 49
    Publikationsdatum: 2017-08-25
    Beschreibung: Genes, Vol. 8, Pages 211: Two Archaeal RecJ Nucleases from Methanocaldococcus jannaschii Show Reverse Hydrolysis Polarity: Implication to Their Unique Function in Archaea Genes doi: 10.3390/genes8090211 Authors: Gang-Shun Yi Yang Song Wei-Wei Wang Jia-Nan Chen Wei Deng Weiguo Cao Feng-Ping Wang Xiang Xiao Xi-Peng Liu Bacterial nuclease RecJ, which exists in almost all bacterial species, specifically degrades single-stranded (ss) DNA in the 5′ to 3′ direction. Some archaeal phyla, except Crenarchaea, also encode RecJ homologs. Compared with bacterial RecJ, archaeal RecJ exhibits a largely different amino acid sequence and domain organization. Archaeal RecJs from Thermococcus kodakarensis and Pyrococcus furiosus show 5′→3′ exonuclease activity on ssDNA. Interestingly, more than one RecJ exists in some Euryarchaeota classes, such as Methanomicrobia, Methanococci, Methanomicrobia, Methanobacteria, and Archaeoglobi. Here we report the biochemical characterization of two RecJs from Methanocaldococcus jannaschii, the long RecJ1 (MJ0977) and short RecJ2 (MJ0831) to understand their enzymatic properties. RecJ1 is a 5′→3′ exonuclease with a preference to ssDNA; however, RecJ2 is a 3′→5′ exonuclease with a preference to ssRNA. The 5′ terminal phosphate promotes RecJ1 activity, but the 3′ terminal phosphate inhibits RecJ2 nuclease. Go-Ichi-Ni-San (GINS) complex does not interact with two RecJs and does not promote their nuclease activities. Finally, we discuss the diversity, function, and molecular evolution of RecJ in archaeal taxonomy. Our analyses provide insight into the function and evolution of conserved archaeal RecJ/eukaryotic Cdc45 protein.
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    Thema: Biologie
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  • 50
    Publikationsdatum: 2017-08-30
    Beschreibung: Genes, Vol. 8, Pages 214: Detection of G1138A Mutation of the FGFR3 Gene in Tooth Material from a 180-Year-Old Museological Achondroplastic Skeleton Genes doi: 10.3390/genes8090214 Authors: Lucas Boer Jana Naue Laurens de Rooy Roelof-Jan Oostra Throughout the last four centuries, many anatomical museums across the world have collected teratological specimens that became precious objects. These can be regarded as spirits of the past which have captured the morphology of diseases through time. These valuable and irreplaceable specimens can be perfectly used in contemporary dysmorphological or genetic research. Unfortunately, due to the historical nature of these specimens and the regularly used aggressive preservation fluids, DNA degradation is often present. Furthermore, the use of material for DNA extraction is restricted to preserve the appearance of these valuable museological specimens. Thus, the most challenging part in this perspective is to harvest sufficient DNA of good quality for further testing without damaging the specimens. Besides fixated specimens, most teratological collections contain dried skeletal and teeth materials which are an excellent source to extract DNA. We here present a DNA-based method that enables genetic identification of the G1138A mutation of the FGFR3 gene in a 180-year-old achondroplastic skeleton, confirming the previously morphologically determined disease. Nuclear DNA was extracted from a premolar tooth and the mutation was found using Sanger sequencing of a small region of the FGFR3 gene.
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    Thema: Biologie
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  • 51
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    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publikationsdatum: 2017-09-06
    Beschreibung: Genes, Vol. 8, Pages 220: Zebrafish Xenograft: An Evolutionary Experiment in Tumour Biology Genes doi: 10.3390/genes8090220 Authors: Rachael A. Wyatt Nhu P. V. Trieu Bryan D. Crawford Though the cancer research community has used mouse xenografts for decades more than zebrafish xenografts, zebrafish have much to offer: they are cheap, easy to work with, and the embryonic model is relatively easy to use in high-throughput assays. Zebrafish can be imaged live, allowing us to observe cellular and molecular processes in vivo in real time. Opponents dismiss the zebrafish model due to the evolutionary distance between zebrafish and humans, as compared to mice, but proponents argue for the zebrafish xenograft’s superiority to cell culture systems and its advantages in imaging. This review places the zebrafish xenograft in the context of current views on cancer and gives an overview of how several aspects of this evolutionary disease can be addressed in the zebrafish model. Zebrafish are missing homologs of some human proteins and (of particular interest) several members of the matrix metalloproteinase (MMP) family of proteases, which are known for their importance in tumour biology. This review draws attention to the implicit evolutionary experiment taking place when the molecular ecology of the xenograft host is significantly different than that of the donor.
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    Thema: Biologie
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  • 52
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    American Geophysical Union (AGU)
    Publikationsdatum: 2017-09-12
    Digitale ISSN: 2328-4277
    Thema: Geologie und Paläontologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 53
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    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publikationsdatum: 2017-02-18
    Beschreibung: To complete the duplication of large genomes efficiently, mechanisms have evolved that coordinate DNA unwinding with DNA synthesis and provide quality control measures prior to cell division. Minichromosome maintenance protein 10 (Mcm10) is a conserved component of the eukaryotic replisome that contributes to this process in multiple ways. Mcm10 promotes the initiation of DNA replication through direct interactions with the cell division cycle 45 (Cdc45)-minichromosome maintenance complex proteins 2-7 (Mcm2-7)-go-ichi-ni-san GINS complex proteins, as well as single- and double-stranded DNA. After origin firing, Mcm10 controls replication fork stability to support elongation, primarily facilitating Okazaki fragment synthesis through recruitment of DNA polymerase-α and proliferating cell nuclear antigen. Based on its multivalent properties, Mcm10 serves as an essential scaffold to promote DNA replication and guard against replication stress. Under pathological conditions, Mcm10 is often dysregulated. Genetic amplification and/or overexpression of MCM10 are common in cancer, and can serve as a strong prognostic marker of poor survival. These findings are compatible with a heightened requirement for Mcm10 in transformed cells to overcome limitations for DNA replication dictated by altered cell cycle control. In this review, we highlight advances in our understanding of when, where and how Mcm10 functions within the replisome to protect against barriers that cause incomplete replication.
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    Thema: Biologie
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  • 54
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    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publikationsdatum: 2017-02-18
    Beschreibung: Faithful duplication of the genome is a challenge because DNA is susceptible to damage by a number of intrinsic and extrinsic genotoxins, such as free radicals and UV light. Cells activate the intra-S checkpoint in response to damage during S phase to protect genomic integrity and ensure replication fidelity. The checkpoint prevents genomic instability mainly by regulating origin firing, fork progression, and transcription of G1/S genes in response to DNA damage. Several studies hint that regulation of forks is perhaps the most critical function of the intra-S checkpoint. However, the exact role of the checkpoint at replication forks has remained elusive and controversial. Is the checkpoint required for fork stability, or fork restart, or to prevent fork reversal or fork collapse, or activate repair at replication forks? What are the factors that the checkpoint targets at stalled replication forks? In this review, we will discuss the various pathways activated by the intra-S checkpoint in response to damage to prevent genomic instability.
    Digitale ISSN: 2073-4425
    Thema: Biologie
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  • 55
    Publikationsdatum: 2017-02-18
    Beschreibung: The objective of this study was to identify a panel of microRNAs (miRNAs) differentially expressed in high-grade non-muscle invasive (NMI; TaG3–T1G3) urothelial carcinoma that progress to muscle-invasive disease compared to those that remain non-muscle invasive, whether recurrence happens or not. Eighty-nine high-grade NMI urothelial carcinoma lesions were identified and total RNA was extracted from paraffin-embedded tissue. Patients were categorized as either having a non-muscle invasive lesion with no evidence of progression over a 3-year period or as having a similar lesion showing progression to muscle invasion over the same period. In addition, comparison of miRNA expression levels between patients with and without prior intravesical therapy was performed. Total RNA was pooled for microarray analysis in each group (non-progressors and progressors), and qRT-PCR of individual samples validated differential expression between non-progressive and progressive lesions. MiR-32-5p, -224-5p, and -412-3p were associated with cancer-specific survival. Downregulation of miR-203a-3p and miR-205-5p were significantly linked to progression in non-muscle invasive bladder tumors. These miRNAs include those implicated in epithelial mesenchymal transition, previously identified as members of a panel characterizing transition from the non-invasive to invasive phenotype in bladder tumors. Furthermore, we were able to identify specific miRNAs that are linked to postoperative outcome in patients with high grade NMI urothelial carcinoma of the bladder (UCB) that progressed to muscle-invasive (MI) disease.
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    Thema: Biologie
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  • 56
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    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publikationsdatum: 2017-02-18
    Beschreibung: In recent years, immunotherapy has gained renewed interest as an alternative therapeutic approach for solid tumors. Its premise is based on harnessing the power of the host immune system to destroy tumor cells. Development of immune-mediated therapies, such as vaccines, adoptive transfer of autologous immune cells, and stimulation of host immunity by targeting tumor-evasive mechanisms have advanced cancer immunotherapy. In addition, studies on innate immunity and mechanisms of immune evasion have enhanced our understanding on the immunology of liver cancer. Preclinical and clinical studies with immune-mediated therapies have shown potential benefits in patients with liver cancer. In this review, we summarize current knowledge and recent developments in tumor immunology by focusing on two main primary liver cancers: hepatocellular carcinoma and cholangiocarcinoma.
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    Thema: Biologie
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  • 57
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    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publikationsdatum: 2017-02-21
    Beschreibung: MYC family proteins play fundamental roles in stem and progenitor cell homeostasis, morphogenesis and cancer. As expected for proteins that profoundly affect the fate of cells, the activities of MYC are regulated at a multitude of levels. One mechanism with the potential to broadly affect the activities of MYC is transcriptional antagonism by a group of MYC‐related transcriptional repressors. From this group, the protein MNT has emerged as having perhaps the most far‐reaching impact on MYC activities. In this review, we discuss the current understanding of MNT, its regulation and how, as a MYC antagonist, it functions both as a tumor suppressor and facilitator of MYC‐driven proliferation and oncogenesis.
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    Thema: Biologie
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  • 58
    Publikationsdatum: 2017-02-23
    Beschreibung: Bambara groundnut (Vigna subterranea (L.) Verdc.) is an underutilised legume crop, which has long been recognised as a protein-rich and drought-tolerant crop, used extensively in Sub-Saharan Africa. The aim of the study was to identify quantitative trait loci (QTL) involved in agronomic and drought-related traits using an expression marker-based genetic map based on major crop resources developed in soybean. The gene expression markers (GEMs) were generated at the (unmasked) probe-pair level after cross-hybridisation of bambara groundnut leaf RNA to the Affymetrix Soybean Genome GeneChip. A total of 753 markers grouped at an LOD (Logarithm of odds) of three, with 527 markers mapped into linkage groups. From this initial map, a spaced expression marker-based genetic map consisting of 13 linkage groups containing 218 GEMs, spanning 982.7 cM (centimorgan) of the bambara groundnut genome, was developed. Of the QTL detected, 46% were detected in both control and drought treatment populations, suggesting that they are the result of intrinsic trait differences between the parental lines used to construct the cross, with 31% detected in only one of the conditions. The present GEM map in bambara groundnut provides one technically feasible route for the translation of information and resources from major and model plant species to underutilised and resource-poor crops.
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    Thema: Biologie
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  • 59
    facet.materialart.
    Unbekannt
    American Geophysical Union (AGU)
    Publikationsdatum: 2017-02-25
    Digitale ISSN: 2328-4277
    Thema: Geologie und Paläontologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 60
    Publikationsdatum: 2017-02-25
    Beschreibung: The tightly regulated process of precursor messenger RNA (pre-mRNA) alternative splicing (AS) is a key mechanism in the regulation of gene expression. Defects in this regulatory process affect cellular functions and are the cause of many human diseases. Recent advances in our understanding of splicing regulation have led to the development of new tools for manipulating splicing for therapeutic purposes. Several tools, including antisense oligonucleotides and trans-splicing, have been developed to target and alter splicing to correct misregulated gene expression or to modulate transcript isoform levels. At present, deregulated AS is recognized as an important area for therapeutic intervention. Here, we summarize the major hallmarks of the splicing process, the clinical implications that arise from alterations in this process, and the current tools that can be used to deliver, target, and correct deficiencies of this key pre-mRNA processing event.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 61
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    Unbekannt
    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publikationsdatum: 2017-02-26
    Beschreibung: Myelocytomatosis oncogene (MYC) family members, including cellular MYC (c-Myc), neuroblastoma derived MYC (MYCN), and lung carcinoma derived MYC (MYCL), have all been implicated as key oncogenic drivers in a broad range of human cancers. Beyond cancer, MYC plays an important role in other physiological and pathological processes, namely immunity and immunological diseases. MYC largely functions as a transcription factor that promotes the expression of numerous target genes to coordinate death, proliferation, and metabolism at the cellular, tissue, and organismal levels. It has been shown that the expression of MYC family members is tightly regulated in immune cells during development or upon immune stimulations. Emerging evidence suggests that MYC family members play essential roles in regulating the development, differentiation and activation of immune cells. Through driving the expression of a broad range of metabolic genes in immune cells, MYC family members coordinate metabolic programs to support immune functions. Here, we discuss our understanding of MYC biology in immune system and how modulation of MYC impacts immune metabolism and responses.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 62
    facet.materialart.
    Unbekannt
    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publikationsdatum: 2017-02-28
    Beschreibung: : While the death rate from stroke has continually decreased due to interventions in the hyperacute stage of the disease, long-term disability and institutionalization have become common sequelae in the aftermath of stroke. Therefore, identification of new molecular pathways that could be targeted to improve neurological recovery among survivors of stroke is crucial. Epigenetic mechanisms such as post-translational modifications of histone proteins and microRNAs have recently emerged as key regulators of the enhanced plasticity observed during repair processes after stroke. In this review, we highlight the recent advancements in the evolving field of epigenetics in stroke recovery.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 63
    Publikationsdatum: 2017-02-28
    Beschreibung: In this study, we demonstrate skillful spring forecasts of detrended September Arctic sea ice extent using passive microwave observations of sea ice concentration (SIC) and melt onset (MO). We compare these to forecasts produced using data from a sophisticated melt pond model, and find similar to higher skill values, where the forecast skill is calculated relative to linear trend persistence. The MO forecasts shows the highest skill in March–May, while the SIC forecasts produce the highest skill in June–August, especially when the forecasts are evaluated over recent years (since 2008). The high MO forecast skill in early spring appears to be driven primarily by the presence and timing of open water anomalies, while the high SIC forecast skill appears to be driven by both open water and surface melt processes. Spatial maps of detrended anomalies highlight the drivers of the different forecasts, and enable us to understand regions of predictive importance. Correctly capturing sea ice state anomalies, along with changes in open water coverage appear to be key processes in skillfully forecasting summer Arctic sea ice.
    Digitale ISSN: 2328-4277
    Thema: Geologie und Paläontologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 64
    Publikationsdatum: 2017-03-01
    Beschreibung: Escherichia coli is able to shift between anaerobic and aerobic metabolism by adapting its gene expression, e.g., of metabolic genes, to the new environment. The dynamics of gene expression that result from environmental shifts are limited, amongst others, by the time needed for regulation and transcription elongation. In this study, we examined gene expression dynamics after an anaerobic-to-aerobic shift on a short time scale (0.5, 1, 2, 5, and 10 min) by RNA sequencing with emphasis on delay times and transcriptional elongation rates (TER). Transient expression patterns and timing of differential expression, characterized by delay and elongation, were identified as key features of the dataset. Gene ontology enrichment analysis revealed early upregulation of respiratory and iron-related gene sets. We inferred specific TERs of 89 operons with a mean TER of 42.0 nt/s and mean delay time of 22.4 s. TERs correlate with sequence features, such as codon bias, whereas delay times correlate with the involvement of regulators. The presented data illustrate that at very short times after a shift in oxygenation, extensional changes of the transcriptome, such as temporary responses, can be observed. Besides regulation, TERs contribute to the dynamics of gene expression.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 65
    Publikationsdatum: 2017-03-02
    Beschreibung: Society has set ambitious targets for stabilizing mean global temperature. To attain these targets, it will have to reduce CO 2 emissions to near zero by mid-century and subsequently remove CO 2 from the atmosphere during the latter half of the century. There is a recognized need to develop technologies for CO 2 removal; however, attempts to develop direct air capture systems have faced both energetic and financial constraints. Recently, BioEnergy with Carbon Capture and Storage (BECCS) has emerged as a leading candidate for removing CO 2 from the atmosphere. However, BECCS can have negative consequences on land, nutrient, and water use as well as biodiversity and food production. Here, we describe an alternative approach based on the large-scale industrial production of marine microalgae. When cultivated with proper attention to power, carbon, and nutrient sources, microalgae can be processed to produce a variety of biopetroleum products, including carbon neutral biofuels for the transportation sector and long-lived, potentially carbon-negative construction materials for the built environment. In addition to these direct roles in mitigating and potentially reversing the effects of fossil CO 2 emissions, microalgae can also play an important indirect role. Because microalgae exhibit much higher primary production rates than terrestrial plants, they require much less land area to produce an equivalent amount of bioenergy and/or food. On a global scale, the avoided emissions resulting from displacement of conventional agriculture may exceed the benefits of microalgae biofuels in achieving climate stabilization goals.
    Digitale ISSN: 2328-4277
    Thema: Geologie und Paläontologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 66
    Publikationsdatum: 2017-03-03
    Beschreibung: Gene therapy arises as a great promise for cancer therapeutics due to its potential to silence genes involved in tumor development. In fact, there are some pivotal gene drivers that suffer critical alterations leading to cell transformation and ultimately to tumor growth. In this vein, gene silencing has been proposed as an active tool to selectively silence these molecular triggers of cancer, thus improving treatment. However, naked nucleic acid (DNA/RNA) sequences are reported to have a short lifetime in the body, promptly degraded by circulating enzymes, which in turn speed up elimination and decrease the therapeutic potential of these drugs. The use of nanoparticles for the effective delivery of these silencers to the specific target locations has allowed researchers to overcome this issue. Particularly, gold nanoparticles (AuNPs) have been used as attractive vehicles for the target-specific delivery of gene-silencing moieties, alone or in combination with other drugs. We shall discuss current trends in AuNP-based delivery of gene-silencing tools, considering the promising road ahead without overlooking existing concerns for their translation to clinics.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 67
    facet.materialart.
    Unbekannt
    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publikationsdatum: 2017-03-03
    Beschreibung: During DNA replication many factors can result in DNA replication stress. The DNA replication stress checkpoint prevents the accumulation of replication stress-induced DNA damage and the potential ensuing genome instability. A critical role for post-translational modifications, such as phosphorylation, in the replication stress checkpoint response has been well established. However, recent work has revealed an important role for transcription in the cellular response to DNA replication stress. In this review, we will provide an overview of current knowledge of the cellular response to DNA replication stress with a specific focus on the DNA replication stress checkpoint transcriptional response and its role in the prevention of replication stress-induced DNA damage.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 68
    facet.materialart.
    Unbekannt
    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publikationsdatum: 2017-03-04
    Beschreibung: Innate and acquired chemoresistance exhibited by most tumours exposed to conventional chemotherapeutic agents account for the majority of relapse cases in cancer patients. Such chemoresistance phenotypes are of a multi-factorial nature from multiple key molecular players. The discovery of the RNA interference pathway in 1998 and the widespread gene regulatory influences exerted by microRNAs (miRNAs) and other non-coding RNAs have certainly expanded the level of intricacy present for the development of any single physiological phenotype, including cancer chemoresistance. This review article focuses on the latest research efforts in identifying and validating specific key molecular players from the two main families of non-coding RNAs, namely miRNAs and long non-coding RNAs (lncRNAs), having direct or indirect influences in the development of cancer drug resistance properties and how such knowledge can be utilised for novel theranostics in oncology.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 69
    Publikationsdatum: 2017-03-04
    Beschreibung: n/a
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 70
    Publikationsdatum: 2017-03-04
    Beschreibung: FacioScapuloHumeral muscular Dystrophy (FSHD) is one of the most prevalent hereditary myopathies and is generally characterized by progressive muscle atrophy affecting the face, scapular fixators; upper arms and distal lower legs. The FSHD locus maps to a macrosatellite D4Z4 repeat array on chromosome 4q35. Each D4Z4 unit contains a DUX4 gene; the most distal of which is flanked by a polyadenylation site on FSHD-permissive alleles, which allows for production of stable DUX4 mRNAs. In addition, an open chromatin structure is required for DUX4 gene transcription. FSHD thus results from a gain of function of the toxic DUX4 protein that normally is only expressed in germ line and stem cells. Therapeutic strategies are emerging that aim to decrease DUX4 expression or toxicity in FSHD muscle cells. We review here the heterogeneity of DUX4 mRNAs observed in muscle and stem cells; and the use of antisense oligonucleotides (AOs) targeting the DUX4 mRNA to interfere either with transcript cleavage/polyadenylation or intron splicing. We show in primary cultures that DUX4-targeted AOs suppress the atrophic FSHD myotube phenotype; but do not improve the disorganized FSHD myotube phenotype which could be caused by DUX4c over-expression. Thus; DUX4c might constitute another therapeutic target in FSHD.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 71
    Publikationsdatum: 2017-03-07
    Beschreibung: Notch is indispensable for T cell lineage commitment, and is needed for thymocyte differentiation at early phases. During early stages of T cell development, active Notch prevents other lineage potentials including B cell lineage and myeloid cell (e.g., dendritic cell) lineage. Nevertheless, the precise intracellular signaling pathways by which Notch promotes T cell differentiation remain unclear. Here we report that the transcription factor c‐Myc is a key mediator of the Notch signaling–regulated T cell differentiation. In a well‐established in vitro differentiation model of T lymphocytes from hematopoietic stem cells, we showed that Notch1 and 4 directly promoted c‐Myc expression; dominant‐negative (DN) c‐Myc inhibited early T cell differentiation. Moreover, the c‐Myc expression activated by Notch signaling increased the expression of survivin, an inhibitor of apoptosis (IAP) protein. We further demonstrated that over‐expression of c‐Myc increased the abundance of survivin and the T cell differentiation thereof, whereas dn c‐Myc reduced survivin levels and concomitantly retarded the differentiation. The c‐Myc–dependent survivin induction is functionally germane, because Notch‐dependent T cell differentiation was canceled by the depletion of survivin. These results identify both c‐Myc and survivin as important mediators of the Notch signaling–regulated differentiation of T lymphocytes from hematopoietic stem cells.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 72
    Publikationsdatum: 2017-03-07
    Beschreibung: Short interspersed elements (SINEs) are typically silenced by DNA hypermethylation in somatic cells, but can retrotranspose in proliferating cells during adult neurogenesis. Hypomethylation caused by disease pathology or genotoxic stress leads to genomic instability of SINEs. The goal of the present investigation was to determine whether neurotoxic doses of binge or chronic methamphetamine (METH) trigger retrotransposition of the identifier (ID) element, a member of the rat SINE family, in the dentate gyrus genomic DNA. Adult male Sprague‐Dawley rats were treated with saline or high doses of binge or chronic METH and sacrificed at three different time points thereafter. DNA methylation analysis, immunohistochemistry and next‐generation sequencing (NGS) were performed on the dorsal dentate gyrus samples. Binge METH triggered hypomethylation, while chronic METH triggered hypermethylation of the CpG‐2 site. Both METH regimens were associated with increased intensities in poly(A)‐binding protein 1 (PABP1, a SINE regulatory protein)‐like immunohistochemical staining in the dentate gyrus. The amplification of several ID element sequences was significantly higher in the chronic METH group than in the control group a week after METH, and they mapped to genes coding for proteins regulating cell growth and proliferation, transcription, protein function as well as for a variety of transporters. The results suggest that chronic METH induces ID element retrotransposition in the dorsal dentate gyrus and may affect hippocampal neurogenesis.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 73
    facet.materialart.
    Unbekannt
    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publikationsdatum: 2017-06-03
    Beschreibung: For nearly three decades, R loops have been closely linked with class switch recombination (CSR), the process that generates antibody isotypes and that occurs via a complex cascade initiated by transcription-coupled mutagenesis in switch recombination sequences. R loops form during transcription of switch recombination sequences in vitro and in vivo, and there is solid evidence that R loops are required for efficient class switching. The classical model of R loops posits that they boost mutation rates by generating stable and long tracts of single-stranded DNA that serve as the substrate for activation induced deaminase (AID), the enzyme that initiates the CSR reaction cascade by co-transcriptionally mutating ssDNA in switch recombination sequences. Though logical and compelling, this model has not been supported by in vivo evidence. Indeed, several reports suggest that R loops may not be involved in recruiting AID activity to switch regions, meaning that R loops probably serve other unanticipated roles in CSR. Here, I review the key findings in this field to date and propose hypotheses that could help towards elucidating the precise function of R loops in CSR.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 74
    Publikationsdatum: 2017-06-08
    Beschreibung: Biome-specific soil respiration (Rs) has important yet different roles in both the carbon cycle and climate change from regional to global scales. To date, no comparable studies related to global biome-specific Rs have been conducted applying comprehensive global Rs databases. The goal of this study was to develop artificial neural network (ANN) models capable of spatially estimating global Rs and to evaluate the effects of interannual climate variations on 10 major biomes. We used 1,976 annual Rs field records extracted from global Rs literature to train and test the ANN models. We determined that the best ANN model for predicting biome-specific global annual Rs was the one that applied mean annual temperature (MAT), mean annual precipitation (MAP) and biome type as inputs ( r 2  = 0.60). The ANN models reported an average global Rs of 93.3 ± 6.1 Pg C year −1 from 1960 to 2012 and an increasing trend in average global annual Rs of 0.04 Pg C year −1 . Estimated annual Rs increased with increases in MAT and MAP in cropland, boreal forest, grassland, shrubland and wetland biomes. Additionally, estimated annual Rs decreased with increases in MAT and increased with increases in MAP in desert and tundra biomes, and only significantly decreased with increases in MAT ( r 2  = 0.87) in the savannah biome. The developed biome-specific global Rs database for global land and soil carbon models will aid in understanding the mechanisms underlying variations in soil carbon dynamics and in quantifying uncertainty in the global soil carbon cycle.
    Digitale ISSN: 2328-4277
    Thema: Geologie und Paläontologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 75
    Publikationsdatum: 2017-06-08
    Beschreibung: ABSTRACT Monitoring is science keeping our thumb on the pulse of the environment to detect any changes of concern for societies. Basic science is the question-driven search for fundamental processes and mechanisms. Given the firm root of monitoring in human interests and needs, basic sciences have often been regarded as scientifically “purer” – particularly within university-based research communities. We argue that the dichotomy between “research” and “monitoring” is an artificial one, and that this artificial split clouds the definition of scientific goals and leads to suboptimal use of resources. We claim that the synergy between the two scientific approaches is well distilled by science conducted under extreme logistic constraints, when scientists are forced to take full advantage of both the data and the infrastructure available. In evidence of this view, we present our experiences from two decades of uniting research and monitoring at the remote research facility Zackenberg in High Arctic Greenland. For this site, we show how the combination of insights from monitoring with the mechanistic understanding obtained from basic research has yielded the most complete understanding of the system – to the benefit of all, and as an example to follow. We therefore urge scientists from across the continuum from monitoring to research to come together, to disregard old division lines, and to work together to expose a comprehensive picture of ecosystem change and its consequences.
    Digitale ISSN: 2328-4277
    Thema: Geologie und Paläontologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 76
    facet.materialart.
    Unbekannt
    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publikationsdatum: 2017-06-08
    Beschreibung: Cancer is associated with genomic instability and aging. Genomic instability stimulates tumorigenesis, whereas deregulation of oncogenes accelerates DNA replication and increases genomic instability. It is therefore reasonable to assume a positive feedback loop between genomic instability and oncogenic stress. Consistent with this premise, overexpression of the MYC transcription factor increases the phosphorylation of serine 139 in histone H2AX (member X of the core histone H2A family), which forms so-called γH2AX, the most widely recognized surrogate biomarker of double-stranded DNA breaks (DSBs). Paradoxically, oncogenic MYC can also promote the resistance of cancer cells to chemotherapeutic DNA-damaging agents such as cisplatin, clearly implying an antagonistic role of MYC in genomic instability. In this review, we summarize the underlying mechanisms of the conflicting functions of MYC in genomic instability and discuss when and how the oncoprotein exerts the contradictory roles in induction of DSBs and protection of cancer-cell genomes.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 77
    Publikationsdatum: 2017-06-16
    Beschreibung: n/a
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 78
    Publikationsdatum: 2017-06-18
    Beschreibung: Methylation modifications play an important role in multiple biological processes. Several studies have reported altered methylation patterns in male sterile plants such as rice and wheat, but little is known about the global methylation profiles and their possible roles in the cabbage (Brassica oleracea) male sterile line. In this study, single-base-resolution bisulfite sequencing (BS-Seq) was adopted to identify the pattern and degree of cytosine methylation in the male sterile line 01-20S and its near-isogenic fertile line 01-20F. Similar methylation patterns were profiled, with some changes observed in local positions. In total, 505 differentially methylated genomic regions (DMRs) and 106 DMR-associated genes were detected. Nine genes related to pollen development were discovered and further validated by a quantitative reverse-transcription polymerase chain reaction (qRT-PCR). Among these, four were downregulated in 01-20S. In particular, Bol039180 (an invertase/pectin methylesterase inhibitor family protein) is likely involved in pectin degradation, and might play an important role in the pollen separation defects of 01-20S. This study facilitates a better understanding of DNA methylation alterations and their possible roles in genic male sterility in cabbages.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 79
    Publikationsdatum: 2017-06-04
    Beschreibung: Recently, non-clonal chromosomal alterations previously unappreciated are being proposed to be included in cytogenetic practice. The aim of this inclusion is to obtain a greater understanding of chromosomal instability (CIN) and tumor heterogeneity and their role in cancer evolution and therapy response. Although several genetic assays have allowed the evaluation of the variation in a population of cancer cells, these assays do not provide information at the level of individual cells, therefore limiting the information of the genomic diversity within tumors (heterogeneity). The karyotype is one of the few available cytogenetic techniques that allow us not only to identify the chromosomal alterations present within a single cell, but also allows us to profile both clonal (CCA) and non-clonal chromosomal alterations (NCCAs). A greater understanding of CIN and tumor heterogeneity in cancer could not only improve existing therapeutic regimens but could also be used as targets for the design of new therapeutic approaches. In this review we indicate the importance and significance of karyotypic chaos, NCCAs and CIN in the prognosis of human cancers.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 80
    Publikationsdatum: 2017-06-06
    Beschreibung: Hybrid lethality is a deleterious phenotype that is vital to species evolution. We previously reported hybrid lethality in cabbage (Brassica oleracea) and performed preliminary mapping of related genes. In the present study, the fine mapping of hybrid lethal genes revealed that BoHL1 was located on chromosome C1 between BoHLTO124 and BoHLTO130, with an interval of 101 kb. BoHL2 was confirmed to be between insertion-deletion (InDels) markers HL234 and HL235 on C4, with a marker interval of 70 kb. Twenty-eight and nine annotated genes were found within the two intervals of BoHL1 and BoHL2, respectively. We also applied RNA-Seq to analyze hybrid lethality in cabbage. In the region of BoHL1, seven differentially expressed genes (DEGs) and five resistance (R)-related genes (two in common, i.e., Bo1g153320 and Bo1g153380) were found, whereas in the region of BoHL2, two DEGs and four R-related genes (two in common, i.e., Bo4g173780 and Bo4g173810) were found. Along with studies in which R genes were frequently involved in hybrid lethality in other plants, these interesting R-DEGs may be good candidates associated with hybrid lethality. We also used SNP/InDel analyses and quantitative real-time PCR to confirm the results. This work provides new insight into the mechanisms of hybrid lethality in cabbage.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 81
    Publikationsdatum: 2017-06-08
    Beschreibung: Although recent decades have been the warmest since 1850, and global mean temperatures during 2015 and 2016 beat all instrumental records, the rate of increase in global surface air temperature (GSAT) significantly decreased at the beginning of the 21st Century. In this context, we examine the roles of ice melting and associated increase in sea-water mass, both of which significantly increased at the same time as GSAT decreased. Specifically, we show that (1) the slowdown of the rate of increase in GSAT between the specific periods 1992–2001 and 2002–2011 exists in all three climate records analyzed and is statistically significant at the 5% level amounting between 0.029 and 0. 036 °C/yr and leaving an energy of 14.8 to 18.4 10 19  J/yr available; (2) the increase of the atmosphere-related ice melt between these two periods amounts to 316 Gt/yr which requires 10.5 10 19  J/yr, i.e. between 57% and 71 % of the energy left by the slowdown; and (3) the energy budget shows therefore that the heat required to melt this additional 316 Gt/yr of ice is of the same order as the energy needed to warm the atmosphere during the decade 2002–2011 as much as during the previous one, suggesting a redistribution of heat within the atmosphere-cryosphere system.
    Digitale ISSN: 2328-4277
    Thema: Geologie und Paläontologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 82
    facet.materialart.
    Unbekannt
    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publikationsdatum: 2017-06-13
    Beschreibung: Spinal muscular atrophy (SMA) is a genetic disorder with severity ranging from premature death in infants to restricted motor function in adult life. Despite the genetic cause of this disease being known for over twenty years, only recently has a therapy been approved to treat the most severe form of this disease. Here we discuss the genetic basis of SMA and the subsequent studies that led to the utilization of splice switching oligonucleotides to enhance production of SMN protein, which is absent in patients, through a mechanism of exon inclusion into the mature mRNA. Whilst approval of oligonucleotide-based therapies for SMA should be celebrated, we also discuss some of the limitations of this approach and alternate genetic strategies that are currently underway in clinical trials.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 83
    Publikationsdatum: 2017-06-16
    Beschreibung: One hundred and seventy-three years ago, the last two Great Auks, Pinguinus impennis, ever reliably seen were killed. Their internal organs can be found in the collections of the Natural History Museum of Denmark, but the location of their skins has remained a mystery. In 1999, Great Auk expert Errol Fuller proposed a list of five potential candidate skins in museums around the world. Here we take a palaeogenomic approach to test which—if any—of Fuller’s candidate skins likely belong to either of the two birds. Using mitochondrial genomes from the five candidate birds (housed in museums in Bremen, Brussels, Kiel, Los Angeles, and Oldenburg) and the organs of the last two known individuals, we partially solve the mystery that has been on Great Auk scholars’ minds for generations and make new suggestions as to the whereabouts of the still-missing skin from these two birds.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 84
    Publikationsdatum: 2017-06-18
    Beschreibung: Small interfering RNA (siRNA) duplexes are short (usually 21 to 24 bp) double-stranded RNAs (dsRNAs) with several overhanging nucleotides at both 5′- and 3′-ends. It has been found that siRNA duplexes bind the RNA-induced silencing complex (RISC) and cleave the sense strands with endonucleases. In this study, for the first time, we detected siRNA duplexes induced by plant viruses on a large scale using next-generation sequencing (NGS) data. In addition, we used the detected 21 nucleotide (nt) siRNA duplexes with 2 nt overhangs to construct a dataset for future data mining. The analytical results of the features in the detected siRNA duplexes were consistent with those from previous studies. The investigation of siRNA duplexes is useful for a better understanding of the RNA interference (RNAi) mechanism. It can also help to improve the virus detection based on the small RNA sequencing (sRNA-seq) technologies and to rationally design siRNAs for RNAi experiments.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 85
    Publikationsdatum: 2017-06-03
    Beschreibung: Climate change is a major driver of vegetation activity but its complex ecological relationships impede research efforts. In this study, the spatial distribution and dynamic characteristics of climate change effects on vegetation activity in China from the 1980s to the 2010s and from 2021 to 2050 were investigated using a geographically weighted regression (GWR) model. The GWR model was based on combined datasets of satellite vegetation index, climate observation and projection, and future vegetation productivity simulation. Our results revealed that the significantly positive precipitation-vegetation relationship was and will be mostly distributed in North China. However, the regions with temperature-dominated distribution of vegetation activity were and will be mainly located in South China. Due to the varying climate features and vegetation cover, the spatial correlation between vegetation activity and climate change may be altered. There will be different dominant climatic factors for vegetation activity distribution in some regions such as Northwest China, and even opposite correlations in Northeast China. Additionally, the response of vegetation activity to precipitation will move southward in the next three decades. In contrast, although the high warming rate will restrain the vegetation activity, precipitation variability could modify hydrothermal conditions for vegetation activity. This observation is exemplified in the projected future enhancement of vegetation activity in the Tibetan Plateau and weakened vegetation activity in East and Middle China. Furthermore, the vegetation in most parts of North China may adapt to an arid environment, whereas in many southern areas, vegetation will be repressed by water shortage in the future.
    Digitale ISSN: 2328-4277
    Thema: Geologie und Paläontologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 86
    facet.materialart.
    Unbekannt
    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publikationsdatum: 2017-06-06
    Beschreibung: RNA-binding proteins play fundamental roles in the regulation of molecular processes critical to cellular and organismal homeostasis. Recent studies have identified the RNA-binding protein Ataxin-2 as a genetic determinant or risk factor for various diseases including spinocerebellar ataxia type II (SCA2) and amyotrophic lateral sclerosis (ALS), amongst others. Here, we first discuss the increasingly wide-ranging molecular functions of Ataxin-2, from the regulation of RNA stability and translation to the repression of deleterious accumulation of the RNA-DNA hybrid-harbouring R-loop structures. We also highlight the broader physiological roles of Ataxin-2 such as in the regulation of cellular metabolism and circadian rhythms. Finally, we discuss insight from clinically focused studies to shed light on the impact of molecular and physiological roles of Ataxin-2 in various human diseases. We anticipate that deciphering the fundamental functions of Ataxin-2 will uncover unique approaches to help cure or control debilitating and lethal human diseases.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 87
    Publikationsdatum: 2017-06-07
    Beschreibung: MicroRNAs (miRNAs) are a class of endogenous small noncoding RNAs which regulate diverse molecular and biochemical processes at a post-transcriptional level in plants. As the ancestor of domesticated wheat, wild emmer wheat (Triticum turgidum ssp. dicoccoides) has great genetic potential for wheat improvement. However, little is known about miRNAs and their functions on salinity stress in wild emmer. To obtain more information on miRNAs in wild emmer, we systematically investigated and characterized the salinity-responsive miRNAs using deep sequencing technology. A total of 88 conserved and 124 novel miRNAs were identified, of which 50 were proven to be salinity-responsive miRNAs, with 32 significantly up-regulated and 18 down-regulated. miR172b and miR1120a, as well as mi393a, were the most significantly differently expressed. Targets of these miRNAs were computationally predicted, then Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that the targets of salinity-responsive miRNAs were enriched in transcription factors and stress-related proteins. Finally, we investigated the expression profiles of seven miRNAs ranging between salt-tolerant and sensitive genotypes, and found that they played critical roles in salinity tolerance in wild emmer. Our results systematically identified the salinity-responsive miRNAs in wild emmer, not only enriching the miRNA resource but also laying the foundation for further study on the biological functions and evolution of miRNAs in wild wheat and beyond.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 88
    Publikationsdatum: 2017-06-08
    Beschreibung: We examine some unexpected epistemological conflicts that arise at the interfaces between ecological science, the ecosystem services framework, policy and industry. We use an example from our own research to motivate and illustrate our main arguments, while also reviewing standard approaches to ecological science using the ecosystem services framework. While we agree that the ecosystem services framework has benefits in its industrial applications because it may force economic decision makers to consider a broader range of costs and benefits than they would do otherwise, we find that many alignments of ecology with the ecosystem services framework are asking questions that are irrelevant to real-world applications, and generating data that does not serve real-world applications. We attempt to clarify why these problems arise and how to avoid them. We urge fellow ecologists to reflect on the kind of research that can lead to both scientific advances and applied relevance to society. In our view, traditional empirical approaches at landscape scales or with place-based emphases are necessary to provide applied knowledge for problem solving, which is needed once decision makers identify risks to ecosystem services. We conclude that the ecosystem services framework is a good policy tool when applied to decision-making contexts, but not a good theory either of social valuation or ecological interactions, and should not be treated as one.
    Digitale ISSN: 2328-4277
    Thema: Geologie und Paläontologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 89
    Publikationsdatum: 2017-06-13
    Beschreibung: Adiponectin plays an important role in energy homeostasis and metabolism in mammalian adipose tissue. In this study, the relationship between adiponectin gene (ADIPOQ) haplotypes and variation in growth and carcass traits in New Zealand (NZ) Romney lambs was investigated using General Linear Models (GLMs). Eight haplotypes were found in these lambs and they were composed of the four previously reported promoter fragment sequences (A1–D1) and three previously reported intron 2–exon 3 sequences (A3–C3). The frequencies of the haplotypes ranged from 0.07% to 45.91%. The presence of A1–A3 was associated with a decreased pre-weaning growth rate (p = 0.037), and decreased leg lean-meat yield (p = 0.001), loin lean-meat yield (p = 0.018) and total lean-meat yield (p = 0.004). The presence of A1–C3 was associated with increased carcass fat depth over the 12th rib (V-GR; p = 0.001) and a decreased proportion of loin lean-meat yield (p = 0.045). The presence of B1–A3 was associated with an increased proportion of leg lean-meat yield (p = 0.016) and proportion of shoulder lean-meat yield (p = 0.030). No associations were found with birth weight, tailing weight and weaning weight. These results suggest that ovine ADIPOQ may have value as a genetic marker for NZ Romney sheep breeding.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 90
    Publikationsdatum: 2017-06-28
    Beschreibung: The nascent RNA can reinvade the DNA double helix to form a structure termed the R-loop, where a single-stranded DNA (ssDNA) is accompanied by a DNA-RNA hybrid. Unresolved R-loops can impede transcription and replication processes and lead to genomic instability by a mechanism still not fully understood. In this sense, a connection between R-loops and certain chromatin markers has been reported that might play a key role in R-loop homeostasis and genome instability. To counteract the potential harmful effect of R-loops, different conserved messenger ribonucleoprotein (mRNP) biogenesis and nuclear export factors prevent R-loop formation, while ubiquitously-expressed specific ribonucleases and DNA-RNA helicases resolve DNA-RNA hybrids. However, the molecular events associated with R-loop sensing and processing are not yet known. Given that R-loops hinder replication progression, it is plausible that some DNA replication-associated factors contribute to dissolve R-loops or prevent R-loop mediated genome instability. In support of this, R-loops accumulate in cells depleted of the BRCA1, BRCA2 or the Fanconi anemia (FA) DNA repair factors, indicating that they play an active role in R-loop dissolution. In light of these results, we review our current view of the role of replication-associated DNA repair pathways in preventing the harmful consequences of R-loops.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 91
    Publikationsdatum: 2017-06-28
    Beschreibung: Biotic and abiotic stresses are the major causes of crop loss in lily worldwide. In this study, we retrieved 12 defense-related expressed sequence tags (ESTs) from the NCBI database and cloned, characterized, and established seven of these genes as stress-induced genes in Lilium formolongi. Using rapid amplification of cDNA ends PCR (RACE-PCR), we successfully cloned seven full-length mRNA sequences from L. formolongi line Sinnapal lily. Based on the presence of highly conserved characteristic domains and phylogenetic analysis using reference protein sequences, we provided new nomenclature for the seven nucleotide and protein sequences and submitted them to GenBank. The real-time quantitative PCR (qPCR) relative expression analysis of these seven genes, including LfHsp70-1, LfHsp70-2, LfHsp70-3, LfHsp90, LfUb, LfCyt-b5, and LfRab, demonstrated that they were differentially expressed in all organs examined, possibly indicating functional redundancy. We also investigated the qPCR relative expression levels under two biotic and four abiotic stress conditions. All seven genes were induced by Botrytis cinerea treatment, and all genes except LfHsp70-3 and LfHsp90 were induced by Botrytis elliptica treatment; these genes might be associated with disease tolerance mechanisms in L. formolongi. In addition, LfHsp70-1, LfHsp70-2, LfHsp70-3, LfHsp90, LfUb, and LfCyt-b5 were induced by heat treatment, LfHsp70-1, LfHsp70-2, LfHsp70-3, LfHsp90, and LfCyt-b5 were induced by cold treatment, and LfHsp70-1, LfHsp70-2, LfHsp70-3, LfHsp90, LfCy-b5, and LfRab were induced by drought and salt stress, indicating their likely association with tolerance to these stress conditions. The stress-induced candidate genes identified in this study provide a basis for further functional analysis and the development of stress-resistant L. formolongi cultivars.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 92
    facet.materialart.
    Unbekannt
    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publikationsdatum: 2017-07-01
    Beschreibung: MYC is a pleiotropic transcription factor that controls a number of fundamental cellular processes required for the proliferation and survival of normal and malignant cells, including the cell cycle. MYC interacts with several central cell cycle regulators that control the balance between cell cycle progression and temporary or permanent cell cycle arrest (cellular senescence). Among these are the cyclin E/A/cyclin-dependent kinase 2 (CDK2) complexes, the CDK inhibitor p27KIP1 (p27) and the E3 ubiquitin ligase component S-phase kinase-associated protein 2 (SKP2), which control each other by forming a triangular network. MYC is engaged in bidirectional crosstalk with each of these players; while MYC regulates their expression and/or activity, these factors in turn modulate MYC through protein interactions and post-translational modifications including phosphorylation and ubiquitylation, impacting on MYC’s transcriptional output on genes involved in cell cycle progression and senescence. Here we elaborate on these network interactions with MYC and their impact on transcription, cell cycle, replication and stress signaling, and on the role of other players interconnected to this network, such as CDK1, the retinoblastoma protein (pRB), protein phosphatase 2A (PP2A), the F-box proteins FBXW7 and FBXO28, the RAS oncoprotein and the ubiquitin/proteasome system. Finally, we describe how the MYC/CDK2/p27/SKP2 axis impacts on tumor development and discuss possible ways to interfere therapeutically with this system to improve cancer treatment.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 93
    Publikationsdatum: 2017-07-02
    Beschreibung: Genomic fidelity in the humans is continuously challenged by genotoxic reactive oxygen species (ROS) generated both endogenously during metabolic processes, and by exogenous agents. Mispairing of most ROS-induced oxidized base lesions during DNA replication induces mutations. Although bulky base adducts induced by ultraviolet light and other environmental mutagens block replicative DNA polymerases, most oxidized base lesions do not block DNA synthesis. In 8-oxo-G:A mispairs generated by the incorporation of A opposite unrepaired 8-oxo-G, A is removed by MutYH (MYH) for post-replicative repair, and other oxidized base lesions must be repaired prior to replication in order to prevent mutation fixation. Our earlier studies documented S phase-specific overexpression of endonuclease VIII-like 1 (NEIL1) DNA glycosylase (DG), one of five oxidized base excision repair (BER)-initiating enzymes in mammalian cells, and its high affinity for replication fork-mimicking single-stranded (ss)DNA substrates. We recently provided experimental evidence for the role of NEIL1 in replicating-strand repair, and proposed the “cowcatcher” model of pre-replicative BER, where NEIL1’s nonproductive binding to the lesion base in ssDNA template blocks DNA chain elongation, causing fork regression. Repair of the lesion in the then re-annealed duplex is carried out by NEIL1 in association with the DNA replication proteins. In this commentary, we highlight the critical role of pre-replicative BER in preventing mutagenesis, and discuss the distinction between pre-replicative vs. post-replicative BER.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 94
    Publikationsdatum: 2017-07-08
    Beschreibung: The attrition of telomeres is believed to be a key event not only in mammalian aging, but also in disturbed nutrient sensing, which could lead to numerous metabolic dysfunctions. The current debate focuses mainly on the question whether telomere shortening, e.g., as a heritable trait, may act as a cause or rather represents a consequence of such chronic diseases. This review discusses the damaging events that ultimately may lead or contribute to telomere shortening and can be associated with metabolic diseases.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 95
    Publikationsdatum: 2017-07-13
    Beschreibung: Mutations in the EYS (eyes shut homolog) gene are a common cause of autosomal recessive (ar) retinitis pigmentosa (RP). Without a mammalian model of human EYS disease, there is limited understanding of details of disease expression and rates of progression of the retinal degeneration. We studied clinically and with chromatic static perimetry, spectral-domain optical coherence tomography (OCT), and en face autofluoresence imaging, a cohort of 15 patients (ages 12–51 at first visit), some of whom had longitudinal data of function and structure. Rod sensitivity was able to be measured by chromatic perimetry in most patients at their earliest visits and some patients retained patchy rod function into the fifth decade of life. As expected from RP, cone sensitivity persisted after rod function was no longer measurable. The photoreceptor nuclear layer of the central retina was abnormal except at the fovea in most patients at first visit. Perifoveal disease measured over a period of years indicated that photoreceptor structural loss was followed by dysmorphology of the inner retina and loss of retinal pigment epithelial integrity. Although there could be variability in severity, preliminary analyses of the rates of vision loss suggested that EYS is a more rapidly progressive disease than other ciliopathies causing arRP, such as USH2A and MAK.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 96
    Publikationsdatum: 2017-07-14
    Beschreibung: Because of its low level of energy consumption and the small scale of its industrial development, the Tibet Autonomous Region has historically been excluded from China's reported energy statistics, including those regarding CO 2 emissions. In this paper, we estimate Tibet's energy consumption using limited online documents, and we calculate the 2014 energy-related and process-related CO 2 emissions of Tibet and its seven prefecture-level administrative divisions for the first time. Our results show that 5.52 million tons of CO 2 were emitted in Tibet in 2014; 33% of these emissions are associated with cement production. Tibet's emissions per capita amounted to 1.74 tons in 2014, which is substantially lower than the national average, although Tibet's emission intensity is relatively high at 0.60 tons per thousand yuan in 2014. Among Tibet's seven prefecture-level administrative divisions, Lhasa City and Shannan Region are the two largest CO 2 contributors and have the highest per capita emissions and emission intensities. The Nagqu and Nyingchi regions emit little CO 2 due to their farming/pasturing-dominated economies. This quantitative measure of Tibet's regional CO 2 emissions provides solid data support for Tibet's actions on climate change and emission reductions.
    Digitale ISSN: 2328-4277
    Thema: Geologie und Paläontologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 97
    facet.materialart.
    Unbekannt
    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publikationsdatum: 2017-07-14
    Beschreibung: Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively “novel”. Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 98
    Publikationsdatum: 2017-07-15
    Beschreibung: The cancer atavistic theory suggests that carcinogenesis is a reverse evolution process. It is thus of great interest to explore the evolutionary origins of cancer driver genes and the relevant mechanisms underlying the carcinogenesis. Moreover, the evolutionary features of cancer driver genes could be helpful in selecting cancer biomarkers from high-throughput data. In this study, through analyzing the cancer endogenous molecular networks, we revealed that the subnetwork originating from eukaryota could control the unlimited proliferation of cancer cells, and the subnetwork originating from eumetazoa could recapitulate the other hallmarks of cancer. In addition, investigations based on multiple datasets revealed that cancer driver genes were enriched in genes originating from eukaryota, opisthokonta, and eumetazoa. These results have important implications for enhancing the robustness of cancer prognosis models through selecting the gene signatures by the gene age information.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 99
    Publikationsdatum: 2017-07-18
    Beschreibung: Genes, Vol. 8, Pages 183: Genetic Contribution to Alcohol Dependence: Investigation of a Heterogeneous German Sample of Individuals with Alcohol Dependence, Chronic Alcoholic Pancreatitis, and Alcohol-Related Cirrhosis Genes doi: 10.3390/genes8070183 Authors: Jens Treutlein Josef Frank Fabian Streit Céline Reinbold Dilafruz Juraeva Franziska Degenhardt Liz Rietschel Stephanie Witt Andreas Forstner Monika Ridinger Jana Strohmaier Norbert Wodarz Helene Dukal Jerome Foo Per Hoffmann Stefan Herms Stefanie Heilmann-Heimbach Michael Soyka Wolfgang Maier Wolfgang Gaebel Norbert Dahmen Norbert Scherbaum Bertram Müller-Myhsok Susanne Lucae Marcus Ising Felix Stickel Thomas Berg Ulla Roggenbuck Karl-Heinz Jöckel Henrike Scholz Ulrich Zimmermann Stephan Buch Wolfgang Sommer Rainer Spanagel Benedikt Brors Sven Cichon Karl Mann Falk Kiefer Jochen Hampe Jonas Rosendahl Markus Nöthen Marcella Rietschel The present study investigated the genetic contribution to alcohol dependence (AD) using genome-wide association data from three German samples. These comprised patients with: (i) AD; (ii) chronic alcoholic pancreatitis (ACP); and (iii) alcohol-related liver cirrhosis (ALC). Single marker, gene-based, and pathway analyses were conducted. A significant association was detected for the ADH1B locus in a gene-based approach (puncorrected = 1.2 × 10−6; pcorrected = 0.020). This was driven by the AD subsample. No association with ADH1B was found in the combined ACP + ALC sample. On first inspection, this seems surprising, since ADH1B is a robustly replicated risk gene for AD and may therefore be expected to be associated also with subgroups of AD patients. The negative finding in the ACP + ALC sample, however, may reflect genetic stratification as well as random fluctuation of allele frequencies in the cases and controls, demonstrating the importance of large samples in which the phenotype is well assessed.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 100
    Publikationsdatum: 2017-07-22
    Beschreibung: Genes, Vol. 8, Pages 189: Developmental Expression of HSP60 and HSP10 in the Coilia nasus Testis during Upstream Spawning Migration Genes doi: 10.3390/genes8070189 Authors: Di-An Fang Yan-Feng Zhou Min-Ying Zhang Dong-Po Xu Kai Liu Jin-Rong Duan Heat shock protein 60 (HSP60) and heat shock protein 10 (HSP10) are important chaperones, which have been proven to have essential roles in mediating the correct folding of nuclear encoded proteins imported to mitochondria. Mitochondria are known as the power house of the cell, with which it produces energy and respires aerobically. In this regard, the obtained HSP60 and HSP10 have typical characteristics of the HSP60/10 family signature. Their mRNA transcripts detected were highest during the developmental phase (in April), while the lowest levels were found in the resting phase (after spawning in late July). Additionally, the strongest immunolabeling positive signals were found in the primary spermatocyte, with lower positive staining in secondary sperm cells, and a weak or absent level in the mature sperm. At the electron microscopic level, immunogold particles were localized in the mitochondrial matrix. Data indicated that HSP10 and HSP60 were inducible and functional in the Coilia nasus testis development and migration process, suggesting their essential roles in this process. The results also indicated that HSP60 may be one indicator of properly working mitochondrial import and refolding in the fish testis. This study also provides an expanded perspective on the role of heat shock protein families in spawning migration biology.
    Digitale ISSN: 2073-4425
    Thema: Biologie
    Standort Signatur Erwartet Verfügbarkeit
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